From c0f6f4d1c4d9e1c677710c076324784295b128ce Mon Sep 17 00:00:00 2001 From: Adam Parler <35127748+bigperm17@users.noreply.github.com> Date: Sun, 3 Oct 2021 11:44:57 -0700 Subject: [PATCH 01/11] Initial commit --- .gitignore | 32 +++ LICENSE | 674 +++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 2 + 3 files changed, 708 insertions(+) create mode 100644 .gitignore create mode 100644 LICENSE create mode 100644 README.md diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..259148f --- /dev/null +++ b/.gitignore @@ -0,0 +1,32 @@ +# Prerequisites +*.d + +# Compiled Object files +*.slo +*.lo +*.o +*.obj + +# Precompiled Headers +*.gch +*.pch + +# Compiled Dynamic libraries +*.so +*.dylib +*.dll + +# Fortran module files +*.mod +*.smod + +# Compiled Static libraries +*.lai +*.la +*.a +*.lib + +# Executables +*.exe +*.out +*.app diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..2f152cb --- /dev/null +++ b/README.md @@ -0,0 +1,2 @@ +# nwchem_convert +Converting NWChem code from FORTRAN to C/C++ From 7e8da872a143e165aca4ed14374257136cc3b144 Mon Sep 17 00:00:00 2001 From: Adam Parler <35127748+bigperm17@users.noreply.github.com> Date: Sun, 3 Oct 2021 11:49:12 -0700 Subject: [PATCH 02/11] Added a few files to begin translating --- src/basis/getlibr.py | 64 ++ src/nwchem.cpp | 403 ++++++++ src/rtdb/rtdb.h | 105 ++ src/tce/oce.py | 2273 +++++++++++++++++++++++++++++++++++++++++ src/tce/splitfiles.py | 32 + src/util/errquit.h | 33 + 6 files changed, 2910 insertions(+) create mode 100644 src/basis/getlibr.py create mode 100644 src/nwchem.cpp create mode 100644 src/rtdb/rtdb.h create mode 100644 src/tce/oce.py create mode 100644 src/tce/splitfiles.py create mode 100644 src/util/errquit.h diff --git a/src/basis/getlibr.py b/src/basis/getlibr.py new file mode 100644 index 0000000..c5aefbf --- /dev/null +++ b/src/basis/getlibr.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python3 +# This script downloads the basis set library data from www.basissetexchange.org +# into the directory $NWCHEM_TOP/src/basis/libraries.bse +# to use, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/ +# Requires the installation of the python env. from +# https://github.com/MolSSI-BSE/basis_set_exchange +# See https://molssi-bse.github.io/basis_set_exchange/ +# +# names changed +# def2-universal-jfit was weigend_coulomb_fitting +# dgauss-a1-dftjfit was dgauss_a1_dft_coulomb_fitting +# dgauss-a2-dftjfit was dgauss_a2_dft_coulomb_fitting +# +import basis_set_exchange as bse +from datetime import datetime +today = datetime.now().isoformat(timespec='minutes') +print(today) +all_bs = bse.get_all_basis_names() +md = bse.get_metadata() +for bas_name in all_bs: + #get version and list of elements + version_bs = md[bas_name]['latest_version'] + elements_list = md[bas_name]['versions'][version_bs]['elements'] + #open file + # get rid of asterisks + file_name = bas_name.replace("*","s") + #get rid of parenthesis + file_name = file_name.replace("(","") + file_name = file_name.replace(")","") + #replace commas with underscore + file_name = file_name.replace(",","_") + #replace whitespace with underscore + file_name = file_name.replace(" ","_") + #replace forward slash with underscore + file_name = file_name.replace("/","_") + print(' file name is '+file_name+"\n") + output_file = open(file_name,'w') + output_file.write('# BSE Version '+bse.version()+'\n') + output_file.write('# Data downloaded at '+today+'\n') + output_file.write('# '+bas_name+' version number '+version_bs+'\n') + output_file.write('# Description: '+md[bas_name]['description']+'\n') + output_file.write('# Role: '+md[bas_name]['role']+'\n') + output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# ')) + output_file.write('# \n') + for element in elements_list: + #element='h' + try: + bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True) + except: +# print("failed for"+element) + pass + else: + bs_str=bs_str.replace("BASIS","basis") + bs_str=bs_str.replace("END","end") + bs_str=bs_str.replace("PRINT","") + element_str=bse.misc.compact_elements([element]) + bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name) + #ECP + bs_str=bs_str.replace("ECP","ecp \""+element_str+"_"+bas_name+"\"") + output_file.write(bs_str) + # + print(bas_name+" "+element_str) +print("end") + diff --git a/src/nwchem.cpp b/src/nwchem.cpp new file mode 100644 index 0000000..620af57 --- /dev/null +++ b/src/nwchem.cpp @@ -0,0 +1,403 @@ +#include +#include +#include "errquit.h" +#include "rtdb.h" +#ifdef USE_TCGMSG + #include "tcgmsg.h" +#else + int NODEID; + extern NODEID; +#endif +#include "pstat.h" +#include "util.h" +#include "inp.h" +#include "bgj_common.h" +#include "stdio.h" + int RTDB; + int STACK; + int HEAP; + int GLOBAL; + bool STATUS; + bool OVERIFY, OHARDFAIL; +#ifdef CRAY_T3D + int oldact, fsigctl; +#endif +#ifdef PSCALE + int IO_CODE; +#else + int32_t IO_CODE; +#endif + +// $Id$ + +// ====================================================================================================== +//> \mainpage Northwest Computational Chemistry Package (NWChem) 7.0.2 +//> +//> NWChem is an open-source computational chemistry package distributed under the terms of +//> the Educational Community License (ECL) 2.0 +//> +//> This software and its documentation were developed at the EMSL at Pacific Northwest National Laboratory, +//> a multiprogram national laboratory, operated for the U.S. Department of Energy by Battelle under +//> Contract Number DE-AC05-76RL01830. Support for this work was provided by the Department of Energy +//> Office of Biological and Environmental Research, Office of Basic Energy Science, and the Office of +//> Advanced Scientific Computing. +//> +//> Licensed under the Educational Community License, Version 2.0 (the "License"); you may +//> not use this file except in compliance with the License. You may obtain a copy of the +//> License at https://opensource.org/licenses/ECL-2.0. +//> +//> Unless required by applicable law or agreed to in writing, software distributed under the +//> License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, +//> either express or implied. See the License for the specific language governing +//> permissions and limitations under the License. +//> +//> Further information, including user documentation and forums, may be found at +//> http://www.nwchem-sw.org/. Alternatively, +//> the paper +//> +//> * M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. Van Dam, +//> D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong (2010)
+//> "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations"
+//> Computer Physics Communications, 181, 1477–1489, DOI: 10.1016/j.cpc.2010.04.018 +//> +//> provides details on the codes capabilities. +//> +//> Copyright (c) 1994-2020 Pacific Northwest National Laboratory, Battelle Memorial Institute +//> +//> Environmental Molecular Sciences Laboratory (EMSL)
+//> Pacific Northwest National Laboratory
+//> Richland, WA 99352 + +// ====================================================================================================== + + +int main(){ + char input_filename[nw_max_path_len], rtdb_name[nw_max_path_len]; + double total_wall, total_cpu; + #ifdef USE_OFFLOAD + int ppnout; + bool offload_enabled; + extern offload_enabled; + int offload_device; + extern offload_device; + #endif + + bool ostartup, ocontinue, orestart; + bool input_parse; + extern input_parse; + #if defined(USE_OPENMP) + int omp_get_max_threads; + extern omp_get_max_threads; + #endif + +// Create parallel processes and initialize IPC layer + + pbeginf(); + +// MXINIT is needed by PeIGS and PFFT to initialize +// the communication fabric they use. + + mxinit(); + +// Initialize timers so they are relative to job start + + total_wall = -util_wallsec(); + total_cpu = -util_cpusec(); + +// Only process 0 opens the input file +// (note that ga_nodeid() does not work yet!) + + if (nodeid() == 0){ + +// Get the name of the input file from the command line + + get_input_filename(input_filename); + + try { + FILE * LuIn = fopen(input_filename,'r'); + } + catch { + errquit('nwchem: failed to open the input file', 0, INPUT_ERR); + } + } + else{ + #if !(defined(KSR) || defined(IBM) || defined(FUJITSU_SOLARIS) ||defined(FUJITSU_VPP) ||defined(FUJITSU_VPP64)) + fclose(LuIn); + #endif + } + +// Look for memory directive in the input ... must eventually +// open the rtdb first so that can get memory directive out of that +// if it is not in the input + +// The user input model has well-defined categories of memory, +// each of which has a specific size. How we use these limits +// depends on the platform we are running on. + + input_mem_size(stack, heap, global, overify, ohardfail); + +// Initialize local memory allocator & global array tools + + ga_initialize_ltd(ma_sizeof(mt_dbl,global,mt_byte)); + // this must happen after GA and before MA + util_setup_gpu_affinity(); + if ( ga_uses_ma() ) { + if (!ma_init(mt_dbl, stack, heap+global)){ + errquit('nwchem.F: ma_init failed (ga_uses_ma=T)',911, MA_ERR); + } + } else{ + if (!ma_init(mt_dbl,stack,heap)) { + errquit('nwchem.F: ma_init failed (ga_uses_ma=F)',911, MA_ERR); + } + } + +// Touch OpenMP here so that any runtime initialization happens up-front. +// This ensures that any printout that the OpenMP runtime generates, +// such as affinity information, appears at the top of the output file. +// Otherwise, it might not appear until e.g. the CCSD module, at which +// point it will pollute the output file in an undesirable way. + +// Do not move this in front of GA/MPI/TCGMSG initialization, since the +// OpenMP runtime may inherit affinity information from MPI that is only +// determined during MPI initialization. + +// Format definition is outside of preprocessor protection to ensure the +// label is not accidentally reused, since that will not be caught by +// testing that does not enable OpenMP. + + g99 format(2x, 'NWChem w/ OpenMP: Maximum threads = ',i4); + #if defined(USE_OPENMP){ + #pragma omp parallel + #pragma omp master + { + if (ga_nodeid() == 0){ + write(luout,g99); + omp_get_max_threads(); + } + } + #endif +// set no. threads for threaded BLAS to 1 + util_blas_set_num_threads(1); + + rtdb_init() + +// More for amusement then efficiency force all MA allocated entities +// to be aligned at the beginning of a 128 byte cache line + +// if (!ma_set_numalign(7)){ +// errquit('nwchem.cpp: ma_set_numalign failed',911, MA_ERR); +// } +// aligned to 64byte record + if (!ma_set_numalign(6)){ + errquit('nwchem.cpp: ma_set_numalign failed', 911, MA_ERR); + } + + +//old:------------------------------------------------------- START --------- +//old:C GA allocations come out of MA space, so lump them together +//old:C and let MA impose the limits on GA sizes instead of actually +//old:C using the global limit. +//old:C +//old: if ( ga_uses_ma() ) then +//old: if (.not. ma_init(mt_dbl, stack, heap+global)) +//old: $ call errquit('nwchem: ma_init failed', -1) +//old: call ga_initialize +//old:C +//old:C GA allocations are separate from MA, so the separate limit +//old:C must be enforced. Note GA only understands bytes. +//old:C +//old: else +//old: if (.not. ma_init(mt_dbl, stack, heap)) +//old: $ call errquit('nwchem: ma_init failed', -1) +//old: call ga_initialize_ltd(ma_sizeof(mt_dbl, global, mt_byte) ) +//old: endif +//old:------------------------------------------------------- END ----------- + +//*** call nxtval_ga_initialize() + +// Trap SIGFPE after GA to override handler + +//*** call ieeetrap() + #if defined(LINUXALPHA) + dec_fpe(); // To avoid underflow problems on Alpha in Texas + #endif + #ifdef CRAY_T3D + // This as a temporary fix for SIGFPE in Texas that does not seem + // to affect the final results + oldact = fsigctl('IGNORE','SIGFPE',0); + #endif + #ifdef LINUX +// uncommenting this line turns on sigfpe trapping under linux +// linux_trapfpe(); + #endif + #ifdef MACX +// uncommenting this line turns on sigfpe trapping under Mac OSX +// macx_trapfpe(); + #endif +// Hard fail is good for development but means that we cannot +// respond to allocation problems. Disable by default. + status = ma_set_auto_verify(overify); + status = ma_set_hard_fail(ohardfail); + status = ma_set_error_print(ohardfail); + +// Initialize pstat + + if (!pstat_init(20,1,' ')){ + errquit('nwchem: pstat_init failed', 0, UNKNOWN_ERR); + } + + input_file_info(input_filename, rtdb_name, ostartup, ocontinue); + +// Now are ready to summarize the environment + + nwchem_banner(input_filename, rtdb_name, ostartup, ocontinue); + +// Actually open the database and store the file prefix + +// Note that only process 0 has the database name ... that is OK. + + if (ostartup){ + if (!rtdb_open(rtdb_name, 'empty', rtdb)){ + errquit('start: rtdb_open empty failed', 0, RTDB_ERR); + } + } else{ + if (!rtdb_open(rtdb_name, 'old', rtdb)){ + errquit('start: rtdb_open old failed', 0, RTDB_ERR); + } + } + + +// initialize nxtask + nxtask_init(rtdb); + +//!! BGJ + bgj_rtdb = rtdb; +//!! BGJ + + + if (ostartup || ocontinue){ + orestart = false; + } else{ + orestart = true; + } + + util_set_rtdb_state(rtdb, ostartup, ocontinue, orestart); + util_file_info_rtdb(rtdb); // Save file info for restart + movecs_ecce_print_on(); + geom_hnd_parallel(true) + perfm_start(); + + #ifdef USE_OFFLOAD + util_getppn(ppnout); + if (ppnout == 0){ + errquit('util_getppn failed',0,UERR); + } + if (ga_nodeid() == 0){ + write(luout,*) ga_nodeid(), ' ppn ', ppnout; + } + if (offload_enabled()){ + if (ga_nodeid() < ppnout){ + write(luout, '(I8,A,I2)') ga_nodeid(), ' offload enabled, GPU: ', + offload_device(); + } + } + ga_sync() + #endif + + if (orestart || ocontinue){ + nw_print_restart_info(rtdb); + } + +// if continue then go right to task stored on rtdb do not further parse +// input. if input is required then user should have used restart + + if (ocontinue){ + task(rtdb); + } + +// Parse input data, shove into database and execute tasks + + g10 if (input_parse(rtdb)){ // while(tasks to do) + util_print_rtdb_load(rtdb, ' '); // High level print + if (util_print('tcgmsg', print_never)){ + setdbg(1); + } else{ + setdbg(0); + } + #ifdef CATAMOUNT + util_allocga(); + #endif + + task(rtdb); + goto g10; // end while + } + +// Close the RTDB + + util_print_rtdb_load(rtdb, ' '); // High level print + if (util_print('rtdbvalues', print_debug)){ + if (!rtdb_print(rtdb,true)){ + errquit('control: rtdb_print failed', 0, RTDB_ERR); + } + } else if (util_print('rtdb', print_high)){ + if (! rtdb_print(rtdb, false)){ + errquit('control: rtdb_print failed', 0, RTDB_ERR); + } + } + + if (!rtdb_close(rtdb, 'keep')){ + errquit('nwchem: rtdb_close failed', rtdb, RTDB_ERR); + } + + if (util_print('rtdb', print_high) || util_print('rtdbvalues', print_high)){ + rtdb_print_usage(); // Called after closing so memory leaks apparent + } + +// Tidy up pstat + + if (!pstat_terminate()){ + errquit('nwchem: pstat_terminate failed', 0, UNKNOWN_ERR); + } + +//** nxtval_ga_terminate() + +// Print memory and other info + + ga_sync(); + if (ga_nodeid == 0){ + if (util_print('ga summary', print_default)){ + ga_summarize(0); + } + if (util_print('ga stats', print_default)){ + ga_print_stats(); + write(LuOut,*); + } + + } + + + + + + + + + + + + + + + + + + + + + + + + + + return 0; +} diff --git a/src/rtdb/rtdb.h b/src/rtdb/rtdb.h new file mode 100644 index 0000000..c50f473 --- /dev/null +++ b/src/rtdb/rtdb.h @@ -0,0 +1,105 @@ +// +// Header file for intial FORTRAN interface to RTDB +// (see the C header file rtdb.h for more detail) +// +// All functions return .TRUE. on success, .FALSE. on failure +// +// All functions are also mirrored by routines rtdb_* -> rtdb_par_* +// in which process 0 performs the operation and all other processes +// are broadcast the result of a read and discard writes. +// +// rtdb_max_key ... an integer parameter that defines the maximum +// length of a character string key +// +// rtdb_max_file ... an integer parameter that defines the maximum +// length of a file name +// +// +// logical function rtdb_parallel(mode) +// logical mode [input] +// +// +// logical function rtdb_open(filename, mode, handle) +// character *(*) filename [input] +// character *(*) mode [input] +// integer handle [output] +// +// logical function rtdb_clone(handle, suffix) +// integer handle [input] +// character*(*) suffix [input] +// +// logical function rtdb_close(handle, mode) +// integer handle [input] +// character*(*) mode [input] +// +// logical function rtdb_put(handle, name, ma_type, nelem, array) +// integer handle [input] +// character *(*) name [input] +// integer ma_type [input] +// integer nelem [input] +// array(nelem) [input] +// +// logical function rtdb_get_info(handle, name, ma_type, nelem, date) +// integer handle [input] +// character *(*) name [input] +// integer ma_type [output] +// integer nelem [output] +// character*26 date [output] +// +// logical function rtdb_get(handle, name, ma_type, nelem, array) +// integer handle [input] +// character *(*) name [input] +// integer ma_type [input] +// integer nelem [input] +// array(nelem) [output] +// +// logical function rtdb_ma_get(handle, name, ma_type, nelem, ma_handle) +// integer handle [input] +// character *(*) name [input] +// integer ma_type [output] +// integer nelem [output] +// integer ma_handle [output] +// +// logical function rtdb_cput(handle, name, nelem, buf) +// integer handle [input] +// character *(*) name [input] +// character *(*) buf [input] +// +// logical function rtdb_cget(handle, name, nelem, buf) +// integer handle [input] +// character *(*) name [input] +// character *(*) buf [output] +// +// logical function rtdb_print(handle, print_values) +// integer handle [input] +// logical print_values [input] +// +// logical function rtdb_first(handle, name) +// integer handle [input] +// character *(*) name [output] +// +// logical function rtdb_next(handle, name) +// integer handle [input] +// character *(*) name [output] +// +// logical function rtdb_delete(handle, name) +// integer handle [input] +// character *(*) name [input] +// +bool rtdb_open, rtdb_close, rtdb_put, rtdb_get, rtdb_ma_get, + rtdb_cput, rtdb_cget, rtdb_print, rtdb_get_info, + rtdb_first, rtdb_next, rtdb_delete, rtdb_parallel, + rtdb_clone,rtdb_getfname,rtdb_cget_size; +//$Id$ +extern rtdb_open, rtdb_close, rtdb_put, rtdb_get, rtdb_ma_get, + rtdb_cput, rtdb_cget, rtdb_print, rtdb_get_info, + rtdb_first, rtdb_next, rtdb_delete, rtdb_parallel, + rtdb_clone,rtdb_getfname,rtdb_cget_size; +// +// Check these values against rtdb_f2c.c +// +const int rtdb_max_key=255; +const int rtdb_max_file=255; +// +const bool rtdb_seq_mode = false; +const bool rtdb_par_mode = true; diff --git a/src/tce/oce.py b/src/tce/oce.py new file mode 100644 index 0000000..bba8979 --- /dev/null +++ b/src/tce/oce.py @@ -0,0 +1,2273 @@ +# Operator Contraction Engine v.1.0 +# (c) All rights reserved by Battelle & Pacific Northwest Nat'l Lab (2002) +# $Id$ + +import string + +import copy + +import sys + +def readfromfile(filename): + """Converts the content of a file to a ListOperatorSequences object""" + + result = ListOperatorSequences() + file = open(filename,"r") + alwaystrue = 1 + while (alwaystrue): + line = file.readline() + if (line == ""): + file.close() + return result + else: + line = line[0:len(line)-1] + result.add(stringtooperatorsequence(line)) + +def stringtooperatorsequence(expression): + """Converts a string to an operatorsequence object""" + # Syntax of the string is rather loosely defined as: + # (1) Numerical factor (with no permutation allowed) (optional), summation (optional), amplitudes (optional), normal ordered sequence, + # (2) Numerical factor can be an arithmatic expression such as (1.0/4.0), + # (3) Summation starts with either "SUM" or "sum" followed by a parenthesis of indexes, + # (4) Indexes can be either in one-letter notation (a-h, A-H for virtuals, i-o, I-O for occupieds, p-z, P-Z for either, case matters) + # or in OCE notation (p1,p2 for virtuals, h3,h4 for occupieds, g5,g6 for either, no overlap in numbering) + # (5) Amplitudes start with "t" or any name followed by a dagger ("+") indicating complex conjugate (optional) and a parenthesis of indexes, + # (6) Normal ordered operator sequence must exist even when it is empty "{}". + # (7) An example is: (1.0/16.0) Sum (p q r s c d k l) v(p q r s) t(c d k l) {i+ j+ b a}{p+ q+ s r}{c+ d+ l k} + + sequences = expression[expression.index("{"):] + expression = expression[0:expression.index("{")] + operatorlist = [] + # first we decipher normal ordered operator sequence and define operators with/without daggers + newsequences = [] + while (string.find(sequences,"{") != -1): + sequences = sequences[0:string.find(sequences,"{")] + sequences[string.find(sequences,"{")+1:] + if (sequences[len(sequences)-1] != "}"): + raise RuntimeError("Syntax error: the string must end with a normal ordered operator sequence") + sequences = sequences[0:len(sequences)-1] + sequences = string.split(sequences,"}") + for sequence in sequences: + newsequence = [] + sequence = string.split(sequence) + for index in sequence: + if (index[len(index)-1] == "+"): + dagger = "creation" + index = index[0:len(index)-1] + else: + dagger = "annihilation" + if (len(index) == 1): + # one letter notation (vir: a-h & A-H; occ: i-o & I-O; gen: p-z & P-Z) + if (((index >= "a") and (index <= "h")) or ((index >= "A") and (index <= "H"))): + newsequence.append(Operator("particle",dagger,string.ascii_letters.index(index)+1)) + elif (((index >= "i") and (index <= "o")) or ((index >= "I") and (index <= "O"))): + newsequence.append(Operator("hole",dagger,string.ascii_letters.index(index)+1)) + elif (((index >= "p") and (index <= "z")) or ((index >= "P") and (index <= "Z"))): + newsequence.append(Operator("general",dagger,string.ascii_letters.index(index)+1)) + else: + if (index[0] == "p"): + newsequence.append(Operator("particle",dagger,int(index[1:]))) + elif (index[0] == "h"): + newsequence.append(Operator("hole",dagger,int(index[1:]))) + elif (index[0] == "g"): + newsequence.append(Operator("general",dagger,int(index[1:]))) + else: + print("Syntax error: an operator not recognized") + stop + operatorlist = operatorlist + newsequence + newsequences.append(newsequence) + + breakdown = string.split(expression) + + # get a numerical factor if any + numericalfactor = "" + for element in breakdown: + if (((element[0] >= 'a') and (element[0] <= 'z')) or \ + ((element[0] >= 'A') and (element[0] <= 'Z'))): + break + numericalfactor = string.join([numericalfactor, element]) + if (numericalfactor == ""): + numericalfactor = Factor([1.0],[[]]) + else: + numericalfactor = eval(numericalfactor) + numericalfactor = Factor([numericalfactor],[[]]) + + # get a summation if any + summationindexes = "" + remainder = "" + join = 0 + for element in breakdown: + if ((element[0:3] == "SUM") or (element[0:3] == "sum") or (element[0:3] == "Sum")): + join = 1 + if (join == 1): + summationindexes = string.join([summationindexes,element]) + elif (join == 2): + remainder = string.join([remainder,element]) + if ((join == 1) and (")" in element)): + join = 2 + index = string.find(summationindexes,"sum") + if (index != -1): + summationindexes = summationindexes[0:index] + summationindexes[index+3:] + index = string.find(summationindexes,"SUM") + if (index != -1): + summationindexes = summationindexes[0:index] + summationindexes[index+3:] + index = string.find(summationindexes,"Sum") + if (index != -1): + summationindexes = summationindexes[0:index] + summationindexes[index+3:] + index = string.find(summationindexes,"(") + if (index != -1): + summationindexes = summationindexes[0:index] + summationindexes[index+1:] + index = string.find(summationindexes,")") + if (index != -1): + summationindexes = summationindexes[0:index] + summationindexes[index+1:] + summationindexes = string.split(summationindexes) + summation = Summation([]) + for index in summationindexes: + if (len(index) == 1): + # one letter notation (vir: a-h & A-H; occ: i-o & I-O; gen: p-z & P-Z) + if (((index >= "a") and (index <= "h")) or ((index >= "A") and (index <= "H"))): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "particle") and (indexinthelist.index == string.ascii_letters.index(index)+1)): + summation.indexes.append(indexinthelist) + break + elif (((index >= "i") and (index <= "o")) or ((index >= "I") and (index <= "O"))): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "hole") and (indexinthelist.index == string.ascii_letters.index(index)+1)): + summation.indexes.append(indexinthelist) + break + elif (((index >= "p") and (index <= "z")) or ((index >= "P") and (index <= "Z"))): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "general") and (indexinthelist.index == string.ascii_letters.index(index)+1)): + summation.indexes.append(indexinthelist) + break + else: + if (index[0] == "p"): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "particle") and (indexinthelist.index == int(index[1:]))): + summation.indexes.append(indexinthelist) + break + elif (index[0] == "h"): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "hole") and (indexinthelist.index == int(index[1:]))): + summation.indexes.append(indexinthelist) + break + elif (index[0] == "g"): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "general") and (indexinthelist.index == int(index[1:]))): + summation.indexes.append(indexinthelist) + break + else: + print("syntax error") + stop + + # get amplitudes + remainder = string.split(remainder,")") + tobeamplitudes = remainder[0:len(remainder)-1] + remainder = remainder[len(remainder)-1] + amplitudes = [] + for tobeamplitude in tobeamplitudes: + newamplitude = Amplitude() + tobeamplitude = string.split(tobeamplitude,"(") + type = tobeamplitude[0] + conjugate = 1 + lastdaggerposition = len(type) + for i in range(len(type)-1,-1,-1): + if (type[i] == "+"): + conjugate = - conjugate + lastdaggerposition = i + if (conjugate == -1): + newamplitude.conjugate = 1 + else: + newamplitude.conjugate = 0 + newamplitude.type = string.strip(type[0:lastdaggerposition]) + index = 0 + for amplitude in amplitudes: + if ((amplitude.type == newamplitude.type) and (amplitude.index > index)): + index = amplitude.index + newamplitude.index = index + 1 + tobeamplitudeindexes = string.split(tobeamplitude[1]) + newamplitude.indexes = [] + for index in tobeamplitudeindexes: + if (len(index) == 1): + # one letter notation (vir: a-h & A-H; occ: i-o & I-O; gen: p-z & P-Z) + if (((index >= "a") and (index <= "h")) or ((index >= "A") and (index <= "H"))): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "particle") and (indexinthelist.index == string.ascii_letters.index(index)+1)): + newamplitude.indexes.append(indexinthelist) + break + elif (((index >= "i") and (index <= "o")) or ((index >= "I") and (index <= "O"))): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "hole") and (indexinthelist.index == string.ascii_letters.index(index)+1)): + newamplitude.indexes.append(indexinthelist) + break + elif (((index >= "p") and (index <= "z")) or ((index >= "P") and (index <= "Z"))): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "general") and (indexinthelist.index == string.ascii_letters.index(index)+1)): + newamplitude.indexes.append(indexinthelist) + break + else: + if (index[0] == "p"): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "particle") and (indexinthelist.index == int(index[1:]))): + newamplitude.indexes.append(indexinthelist) + break + elif (index[0] == "h"): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "hole") and (indexinthelist.index == int(index[1:]))): + newamplitude.indexes.append(indexinthelist) + break + elif (index[0] == "g"): + for indexinthelist in operatorlist: + if ((indexinthelist.type == "general") and (indexinthelist.index == int(index[1:]))): + newamplitude.indexes.append(indexinthelist) + break + else: + print("syntax error") + stop + amplitudes.append(newamplitude) + + newoperatorsequence = OperatorSequence(numericalfactor,summation,amplitudes,newsequences) + return newoperatorsequence + +def combinepermutations(one,two): + """Connects two permutations of indexes""" + if (len(one) != len(two)): + print("Internal error") + stop + three = [] + for n in range(len(one)/2): + three.append(one[n]) + for n in range(len(one)/2,len(one)): + for m in range(len(two)/2): + if (one[n].isidenticalto(two[m])): + three.append(two[m+len(two)/2]) + return three + +def isidenticalto(one,two): + """Returns true if two permutations of indexes are identical""" + if ((one == []) and (two == [])): + return 1 + if (one == []): + for m in range(len(two)/2): + if (not two[m].isidenticalto(two[m+len(two)/2])): + return 0 + return 1 + if (two == []): + for m in range(len(one)/2): + if (not one[m].isidenticalto(one[m+len(one)/2])): + return 0 + return 1 + if (len(one) != len(two)): + return 0 + for n in range(len(one)/2): + found = 0 + for m in range(len(two)/2): + if ((one[n].isidenticalto(two[m])) and (one[n+len(one)/2].isidenticalto(two[m+len(two)/2]))): + found = 1 + if (not found): + return 0 + return 1 + +class Operator: + + def __init__(self,type="unknown",dagger="unknown",index=0): + """Creates a second-quantized hole/particle/general creation/annihilation operator""" + self.type = type + self.dagger = dagger + self.index = index + + def __str__(self): + """Prints the content""" + return self.show() + + def show(self): + """Returns a human-friendly string of the content""" + show = string.join([self.type[0], repr(self.index)], "") + if (self.dagger == "creation"): + show = string.join([show, "+"], "") + return show + + def tex(self): + """Returns a LaTex form of output""" + show = string.join([self.type[0],"_{",repr(self.index),"}"], "") + if (self.dagger == "creation"): + show = string.join([show, "^{\dagger}"], "") + return show + + def duplicate(self): + """Returns a deepcopy of self""" + duplicate = Operator(self.type,self.dagger,self.index) + return duplicate + + def isidenticalto(self,another): + """Checks if two second-quantized operators are identical""" + if ((self.type == another.type) and (self.dagger == another.dagger) and (self.index == another.index)): + return 1 + else: + return 0 + + def issimilarto(self,another): + """Checks if two second-quantized operators are similar""" + if ((self.type == another.type) and (self.dagger == another.dagger)): + return 1 + else: + return 0 + + def isin(self,list): + """Returns true if an operator is in the list""" + for index in list: + if (self.isidenticalto(index)): + return 1 + return 0 + + def showwithoutdagger(self): + """Returns a human-friendly string of the content""" + show = string.join([self.type[0], repr(self.index)], "") + return show + + def texwithoutdagger(self): + """Returns a human-friendly string of the content""" + show = string.join([self.type[0],"_{",repr(self.index),"}"], "") + return show + + def isgreaterthan(self,another,operatorsequence): + """Returns true if self should be to the right of another in the canonical order""" + + if ((self.type == 'hole') and (another.type == 'particle')): + return 0 + elif ((self.type == 'hole') and (another.type == 'general')): + return 0 + elif ((self.type == 'particle') and (another.type == 'hole')): + return 1 + elif ((self.type == 'particle') and (another.type == 'general')): + return 0 + elif ((self.type == 'general') and (another.type == 'hole')): + return 1 + elif ((self.type == 'general') and (another.type == 'particle')): + return 1 + + # at this point, self.type = another.type + if ((not operatorsequence.summation.hastheindex(self)) and (not operatorsequence.summation.hastheindex(another))): + if (self.index > another.index): + return 1 + else: + return 0 + elif (operatorsequence.summation.hastheindex(self) and (not operatorsequence.summation.hastheindex(another))): + return 0 + elif ((not operatorsequence.summation.hastheindex(self)) and operatorsequence.summation.hastheindex(another)): + return 1 + else: + # at this point, self.type = another.type and both are summed over + selfconnectivity = [] + anotherconnectivity = [] + for namplitude in range(len(operatorsequence.amplitudes)): + amplitude = operatorsequence.amplitudes[namplitude] + if (amplitude.hastheindex(self)): + selfconnectivity.append(namplitude) + for namplitude in range(len(operatorsequence.amplitudes)): + amplitude = operatorsequence.amplitudes[namplitude] + if (amplitude.hastheindex(another)): + anotherconnectivity.append(namplitude) + selfconnectivity.sort() + anotherconnectivity.sort() + if (selfconnectivity < anotherconnectivity): + return 1 + elif (anotherconnectivity < selfconnectivity): + return 0 + + return 0 + +class Summation: + + def __init__(self,indexes=[]): + """Creates a summation""" + self.indexes = indexes + + def __str__(self): + """Print the amplitude""" + return self.show() + + def show(self): + """Returns a human-friendly string of the content""" + show = "Sum (" + for index in self.indexes: + show = string.join([show, index.showwithoutdagger()]) + show = string.join([show,")"]) + return show + + def tex(self): + """Returns a LaTeX string of the content""" + show = "" + for index in self.indexes: + if (show): + show = string.join([show,","],"") + else: + show = "\\sum_{" + show = string.join([show,index.texwithoutdagger()]) + show = string.join([show,"}"]) + return show + + def duplicate(self): + """Returns a deepcopy of itself""" + duplicate = Summation([]) + for index in self.indexes: + duplicate.indexes.append(index.duplicate()) + return duplicate + + def hasthesameform(self,another): + """Checks if two summations have the same numbers of holes, particles, and generals""" + nself = 0 + for operator in self.indexes: + if (operator.type == "hole"): + nself = nself + 1 + nanother = 0 + for operator in another.indexes: + if (operator.type == "hole"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + nself = 0 + for operator in self.indexes: + if (operator.type == "particle"): + nself = nself + 1 + nanother = 0 + for operator in another.indexes: + if (operator.type == "particle"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + nself = 0 + for operator in self.indexes: + if (operator.type == "general"): + nself = nself + 1 + nanother = 0 + for operator in another.indexes: + if (operator.type == "general"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + return 1 + + def isidenticalto(self,another): + """Returns true if two summations are identical""" + if (len(self.indexes) != len(another.indexes)): + return 0 + else: + for nindex in range(len(self.indexes)): + selfindex = self.indexes[nindex] + anotherindex = another.indexes[nindex] + if (not selfindex.isidenticalto(anotherindex)): + return 0 + return 1 + + def hastheindex(self,another): + """Returns true if the summation has the input index""" + has = 0 + for index in self.indexes: + if (index.isidenticalto(another)): + has = 1 + return has + +class Amplitude: + + def __init__(self,type="unknown",indexes=[],index=0,conjugate=0): + """Creates an integral/amplitude""" + self.type = type + self.indexes = indexes + self.index = index + self.conjugate = conjugate + + def __str__(self): + """Print the amplitude""" + return self.show() + + def show(self): + """Returns a human-friendly string of the content""" + show = self.type + if (self.conjugate): + show = string.join([show, "+"],"") + show = string.join([show, "("]) + for index in self.indexes: + show = string.join([show, index.showwithoutdagger()]) + show = string.join([show,")"]) + return show + + def hastheindex(self,another): + """Returns true if the summation has the input index""" + has = 0 + for index in self.indexes: + if (index.isidenticalto(another)): + has = 1 + return has + + def tex(self): + """Returns a LaTeX string of the content""" + show = self.type + show = string.join([show, "^{"]) + for index in self.indexes[0:len(self.indexes)/2]: + show = string.join([show, index.texwithoutdagger()]) + show = string.join([show,"}"]) + show = string.join([show, "_{"]) + for index in self.indexes[len(self.indexes)/2:len(self.indexes)]: + show = string.join([show, index.texwithoutdagger()]) + show = string.join([show,"}"]) + if (self.conjugate): + show = string.join(["\\left(",show,"\\right)^{\\dagger}"],"") + return show + + def duplicate(self): + """Returns a deepcopy of itself""" + duplicate = Amplitude(self.type,[],self.index,self.conjugate) + for index in self.indexes: + duplicate.indexes.append(index.duplicate()) + return duplicate + + def hasthesameform(self,another): + """Checks if two amplitude sets have the same numbers of holes, particles, and generals""" + if (self.type != another.type): + return 0 + if (len(self.indexes) != len(another.indexes)): + return 0 + if (self.conjugate != another.conjugate): + return 0 + nself = 0 + for operator in self.indexes: + if (operator.type == "hole"): + nself = nself + 1 + nanother = 0 + for operator in another.indexes: + if (operator.type == "hole"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + nself = 0 + for operator in self.indexes: + if (operator.type == "particle"): + nself = nself + 1 + nanother = 0 + for operator in another.indexes: + if (operator.type == "particle"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + nself = 0 + for operator in self.indexes: + if (operator.type == "general"): + nself = nself + 1 + nanother = 0 + for operator in another.indexes: + if (operator.type == "general"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + return 1 + + def isidenticalto(self,another): + """Returns true if two amplitudes are identical""" + if (self.type != another.type): + return 0 + elif (len(self.indexes) != len(another.indexes)): + return 0 + elif (self.conjugate != another.conjugate): + return 0 + else: + for nindex in range(len(self.indexes)): + selfindex = self.indexes[nindex] + anotherindex = another.indexes[nindex] + if (not selfindex.isidenticalto(anotherindex)): + return 0 + return 1 + + def isgreaterthan(self,another,operatorsequence): + """Returns true if self should be to the right of another in the canonical order""" + + # count the number of like amplitudes in operatorsequence + nself = 0 + for amplitude in operatorsequence.amplitudes: + if ((amplitude.type == self.type) and (len(amplitude.indexes) == len(self.indexes)) and (amplitude.conjugate == self.conjugate)): + nself = nself + 1 + nanother = 0 + for amplitude in operatorsequence.amplitudes: + if ((amplitude.type == another.type) and (len(amplitude.indexes) == len(another.indexes)) and (amplitude.conjugate == another.conjugate)): + nanother = nanother + 1 + if (nself > nanother): + return 0 + elif (nself < nanother): + return 1 + # conjugate + if (self.conjugate > another.conjugate): + return 0 + elif (self.conjugate < another.conjugate): + return 1 + # type + if (self.type > another.type): + return 1 + elif (self.type < another.type): + return 0 + # number of indexes + if (len(self.indexes) < len(another.indexes)): + return 1 + elif (len(self.indexes) > len(another.indexes)): + return 0 + # number of external indexes + nself = 0 + iself = 9999999999 + for operator in self.indexes: + if (not operatorsequence.summation.hastheindex(operator)): + nself = nself + 1 + if (iself > operator.index): + iself = operator.index + nanother = 0 + ianother = 9999999999 + for operator in another.indexes: + if (not operatorsequence.summation.hastheindex(operator)): + nanother = nanother + 1 + if (ianother > operator.index): + ianother = operator.index + if (nself < nanother): + return 1 + elif (nself > nanother): + return 0 + # earliest external indexes +# if (nself > 0): +# if (ianother > iself): +# return 0 +# elif (ianother < iself): +# return 1 + # connectivity + selfconnectivity = [] + anotherconnectivity = [] + for operator in self.indexes: + if (operatorsequence.summation.hastheindex(operator)): + for amplitude in operatorsequence.amplitudes: + if (amplitude.hastheindex(operator)): + amplitudesymbol = amplitude.type + repr(len(amplitude.indexes)) + if (amplitude.conjugate): + amplitudesymbol = amplitudesymbol + "+" + selfconnectivity.append(amplitudesymbol) + for operator in another.indexes: + if (operatorsequence.summation.hastheindex(operator)): + for amplitude in operatorsequence.amplitudes: + if (amplitude.hastheindex(operator)): + amplitudesymbol = amplitude.type + repr(len(amplitude.indexes)) + if (amplitude.conjugate): + amplitudesymbol = amplitudesymbol + "+" + anotherconnectivity.append(amplitudesymbol) + selfconnectivity.sort() + anotherconnectivity.sort() + if (selfconnectivity < anotherconnectivity): + return 1 + elif (anotherconnectivity < selfconnectivity): + return 0 + return 0 + + def canonicalize(self,operatorsequence): + """Reorder the indexes in the canonical order""" + + another = self.duplicate() + parity = 1 + done = 0 + while (not done): + done = 1 + # reorder super indexes + for noperatora in range(len(another.indexes)/2): + for noperatorb in range(len(another.indexes)/2): + if (noperatora >= noperatorb): + continue + operatora = another.indexes[noperatora] + operatorb = another.indexes[noperatorb] + if (operatora.isgreaterthan(operatorb,operatorsequence)): + another.indexes[noperatorb] = copy.deepcopy(operatora) + another.indexes[noperatora] = copy.deepcopy(operatorb) + parity = parity * (-1) + done = 0 + done = 0 + while (not done): + done = 1 + # reorder sub indexes + for noperatora in range(len(another.indexes)/2,len(another.indexes)): + for noperatorb in range(len(another.indexes)/2,len(another.indexes)): + if (noperatora >= noperatorb): + continue + operatora = another.indexes[noperatora] + operatorb = another.indexes[noperatorb] + if (operatora.isgreaterthan(operatorb,operatorsequence)): + another.indexes[noperatorb] = copy.deepcopy(operatora) + another.indexes[noperatora] = copy.deepcopy(operatorb) + parity = parity * (-1) + done = 0 + + return [another,parity] + +class Factor: + + def __init__(self,coefficients=[],permutations=[]): + """Creates a numerical and permutation factor of an operator sequence""" + self.coefficients = coefficients + self.permutations = copy.deepcopy(permutations) + + def __str__(self): + """Prints the content""" + return self.show() + + def show(self): + """Returns a human-friendly string of contests""" + show = "[" + for n in range(len(self.coefficients)): + coefficient = self.coefficients[n] + # str() rounds a float after 12 digits, while repr() after 17, + # so the former tends to give a more pleasant expression. +# num = rationaltofractional(coefficient)[0] +# den = rationaltofractional(coefficient)[1] +# if (num >= 0): +# show = string.join([show,"+",repr(num)]) +# elif (num < 0): +# show = string.join([show,"-",repr(-num)]) +# if (den != 1): +# show = string.join([show,"/",repr(den)],"") + if (coefficient >= 0.0): + show = string.join([show,"+",str(coefficient)]) + elif (coefficient < 0.0): + show = string.join([show,"-",str(-coefficient)]) + if (self.permutations[n]): + show = string.join([show,"* P("]) + for noperator in range(len(self.permutations[n])/2): + operator = self.permutations[n][noperator] + show = string.join([show,operator.showwithoutdagger()]) + show = string.join([show,"=>"]) + for noperator in range(len(self.permutations[n])/2,len(self.permutations[n])): + operator = self.permutations[n][noperator] + show = string.join([show,operator.showwithoutdagger()]) + show = string.join([show,")"]) + show = string.join([show,"]"]) + return show + + def tex(self): + """Returns a LaTeX string of contests""" + coefficient = self.coefficients[0] + for n in range(len(self.coefficients)): + if (abs(self.coefficients[n]) != abs(coefficient)): + raise RuntimeError("unrealistic factor") + fraction = abs(int(1.0/coefficient)) + if (1.0/float(fraction) != abs(coefficient)): + print(" !!! WARNING !!! inaccurate arithmatic") + if (fraction == 1): + frac = "" + else: + frac = string.join(["\\frac{1}{",str(fraction),"}"],"") + if (coefficient >= 0.0): + show = string.join(["+",frac]) + elif (coefficient < 0.0): + show = string.join(["-",frac]) + if (len(self.coefficients) > 1): + show = string.join([show,"\\left("],"") + for n in range(len(self.coefficients)): + if (self.coefficients[n]/coefficient > 0.0): + show = string.join([show,"+"],"") + else: + show = string.join([show,"-"],"") + if (self.permutations[n]): + show = string.join([show,"P^{"]) + for nindex in range(len(self.permutations[n])/2,3*len(self.permutations[n])/4): + index = self.permutations[n][nindex] + show = string.join([show,index.texwithoutdagger()]) + for nindex in range(len(self.permutations[n])/4,len(self.permutations[n])/2): + index = self.permutations[n][nindex] + show = string.join([show,index.texwithoutdagger()]) + show = string.join([show,"}_{"]) + for nindex in range(len(self.permutations[n])/4): + index = self.permutations[n][nindex] + show = string.join([show,index.texwithoutdagger()]) + for nindex in range(3*len(self.permutations[n])/4,len(self.permutations[n])): + index = self.permutations[n][nindex] + show = string.join([show,index.texwithoutdagger()]) + show = string.join([show,"}"]) + else: + show = string.join([show,"1"],"") + show = string.join([show,"\\right)"]) + return show + + def multiply(self,factor): + """Multiply a factor to all coefficients""" + for n in range(len(self.coefficients)): + self.coefficients[n] = self.coefficients[n] * factor + + def add(self,another,factor=1.0): + """Add two Factors together""" + for m in range(len(another.coefficients)): + done = 0 + for n in range(len(self.coefficients)): + if (isidenticalto(self.permutations[n],another.permutations[m])): + if ((self.coefficients[n] < 0.0) and (another.coefficients[m] * factor > 0.0)): + print(" ! Warning ! cancellation of terms occurred ") + if ((self.coefficients[n] > 0.0) and (another.coefficients[m] * factor < 0.0)): + print(" ! Warning ! cancellation of terms occurred ") + self.coefficients[n] = self.coefficients[n] + another.coefficients[m] * factor + done = 1 + if (not done): + self.coefficients.append(another.coefficients[m] * factor) + self.permutations.append(another.permutations[m]) + +class OperatorSequence: + + def __init__(self,factor=[],summation=[],amplitudes=[],sequence=[]): + """Creates a sequence of normal ordered second-quantized operators with some numerical factor, amplitudes, and summation""" + self.factor = factor + self.summation = summation + self.amplitudes = amplitudes + self.sequence = sequence + + def __str__(self): + """Prints the sequence of operator contractions""" + return self.show() + + def show(self): + """Returns a human-friendly string of the content""" + show = self.factor.show() + if (self.summation): + if (len(self.summation.indexes) > 0): + show = string.join([show, "*", self.summation.show()]) + for index in self.amplitudes: + show = string.join([show, "*", index.show()]) + if (self.sequence): + show = string.join([show, "* <0|"]) + for sequence in self.sequence: + show = string.join([show, "{"]) + for operator in sequence: + show = string.join([show, operator.show()]) + show = string.join([show, "}"]) + show = string.join([show, "|0>"]) + return show + + def tex(self): + """Returns a LaTeX string of the content""" + show = self.factor.tex() +# if (self.summation): +# if (len(self.summation.indexes) > 0): +# show = string.join([show, self.summation.tex()]) + for index in self.amplitudes: + show = string.join([show, index.tex()]) + if (self.sequence): + show = string.join([show, "\\langle 0 |"]) + for sequence in self.sequence: + show = string.join([show, "\{"]) + for operator in sequence: + show = string.join([show, operator.tex()]) + show = string.join([show, "\}"]) + show = string.join([show, "|0\\rangle"]) + return show + + def duplicate(self): + """Makes a copy of itself""" + duplicate = OperatorSequence() + duplicate.factor = copy.deepcopy(self.factor) + duplicate.summation = copy.deepcopy(self.summation) + duplicate.amplitudes = copy.deepcopy(self.amplitudes) + duplicate.sequence = copy.deepcopy(self.sequence) + return duplicate + + def writetofile(self,filename): + """Writes the output to a given file""" + file = open(filename,"w") + file.write(self.show()) + file.write("\n") + + def removeemptycurly(self): + """Eliminates all empty curly brackets (curly means a sequence of normal ordered operator in {})""" + + hasempty = 0 + for ncurly in range(len(self.sequence)): + curly = self.sequence[ncurly] + if (not curly): + del self.sequence[ncurly] + hasempty = 1 + break + + if (hasempty): + self.removeemptycurly() + else: + return self + + def alreadycontracted(self): + """Checks if an operator sequence object is fully contracted""" + + # first, we delete all empty {} just in case + self.removeemptycurly() + + # already fully contracted? + if (not self.sequence): + return 1 + else: + return 0 + + def isunabletocontract(self): + """Counts the number of operators and determine if it is possible to give nonzero contraction at the end""" + + # count the number of hole/particle/general creation/annihilation operators + nholecreation = 0 + nholeannihilation = 0 + nparticlecreation = 0 + nparticleannihilation = 0 + ngeneralcreation = 0 + ngeneralannihilation = 0 + for sequence in self.sequence: + for operator in sequence: + if ((operator.type == "hole") and (operator.dagger == "creation")): + nholecreation = nholecreation + 1 + elif ((operator.type == "hole") and (operator.dagger == "annihilation")): + nholeannihilation = nholeannihilation + 1 + if ((operator.type == "particle") and (operator.dagger == "creation")): + nparticlecreation = nparticlecreation + 1 + elif ((operator.type == "particle") and (operator.dagger == "annihilation")): + nparticleannihilation = nparticleannihilation + 1 + if ((operator.type == "general") and (operator.dagger == "creation")): + ngeneralcreation = ngeneralcreation + 1 + elif ((operator.type == "general") and (operator.dagger == "annihilation")): + ngeneralannihilation = ngeneralannihilation + 1 + + # see if enough operators remain for contractions to survive + uncontractable = 0 + if (nholecreation + ngeneralcreation < nholeannihilation): + uncontractable = 1 + if (nholeannihilation + ngeneralannihilation < nholecreation): + uncontractable = 1 + if (nparticlecreation + ngeneralcreation < nparticleannihilation): + uncontractable = 1 + if (nparticleannihilation + ngeneralannihilation < nparticlecreation): + uncontractable = 1 + return uncontractable + + def performcontraction(self): + """Perform a contraction of the left-most operator""" + + # result will be a list of new operator sequence objects + result = ListOperatorSequences() + + # already fully contracted? + if (self.alreadycontracted()): + newsequence = self.duplicate() + result.add(newsequence) + return result + + # no way to contract? + elif ((len(self.sequence) == 1) or (self.isunabletocontract())): + return result + + # get the left-most operator + leftmost = self.sequence[0][0] + + # loop over other {} + for ncurly in range(len(self.sequence)): + curly = self.sequence[ncurly] + if (ncurly == 0): + continue + for noperator in range(len(self.sequence[ncurly])): + operator = curly[noperator] + + # only allowed contractions are {h+}{h} and {p}{p+} + if (leftmost.dagger == operator.dagger): + continue + elif ((leftmost.type == "hole") and (operator.type == "particle")): + continue + elif ((leftmost.type == "particle") and (operator.type == "hole")): + continue + elif ((leftmost.type == "hole") and (leftmost.dagger == "annihilation")): + continue + elif ((leftmost.type == "particle") and (leftmost.dagger == "creation")): + continue + elif ((operator.type == "hole") and (operator.dagger == "creation")): + continue + elif ((operator.type == "particle") and (operator.dagger == "annihilation")): + continue + + # check if the indexes can be made to match by virtue of summation + exist = "neither" + for index in self.summation.indexes: + if (leftmost.isidenticalto(index)): + exist = "leftmost" + if (exist == "neither"): + for index in self.summation.indexes: + if (operator.isidenticalto(index)): + exist = "operator" + if (exist == "leftmost"): + + # now contraction is possible --- add a new operator sequence object to result + newsequence = self.duplicate() + + # delete leftmost from the summation indexes + for index in newsequence.summation.indexes: + if (leftmost.isidenticalto(index)): + del newsequence.summation.indexes[newsequence.summation.indexes.index(index)] + + # count the number of operators between leftmost and the current operator and determine the parity + length = len(self.sequence[0][1:]) + curly.index(operator) + for anothercurly in self.sequence[1:]: + if (anothercurly == curly): + break + else: + length = length + len(anothercurly) + parity = (-1)**length + newsequence.factor.multiply(parity) + + # delete the contracted pair from the sequence + del newsequence.sequence[0][0] + del newsequence.sequence[ncurly][noperator] + + # replace any appearance of leftmost by operator + if (operator.type == 'general'): + for namplitude in range(len(newsequence.amplitudes)): + amplitude = newsequence.amplitudes[namplitude] + for nindex in range(len(amplitude.indexes)): + index = amplitude.indexes[nindex] + if (operator.isidenticalto(index)): + newsequence.amplitudes[namplitude].indexes[nindex] = leftmost + for nindex in range(len(newsequence.summation.indexes)): + index = newsequence.summation.indexes[nindex] + if (operator.isidenticalto(index)): + newsequence.summation.indexes[nindex] = leftmost + else: + for namplitude in range(len(newsequence.amplitudes)): + amplitude = newsequence.amplitudes[namplitude] + for nindex in range(len(amplitude.indexes)): + index = amplitude.indexes[nindex] + if (leftmost.isidenticalto(index)): + newsequence.amplitudes[namplitude].indexes[nindex] = operator + for nindex in range(len(newsequence.summation.indexes)): + index = newsequence.summation.indexes[nindex] + if (leftmost.isidenticalto(index)): + newsequence.summation.indexes[nindex] = operator + + # cleanup the empty brackets + newsequence.removeemptycurly() + + # add to the result + result.add(newsequence) + + elif (exist == "operator"): + + # contraction is again possible --- add a new operator sequence object to result + newsequence = self.duplicate() + + # delete operator from the summation indexes + for index in newsequence.summation.indexes: + if (operator.isidenticalto(index)): + del newsequence.summation.indexes[newsequence.summation.indexes.index(index)] + + # count the number of operators between leftmost and the current operator and determine the parity + length = len(self.sequence[0][1:]) + curly.index(operator) + for anothercurly in self.sequence[1:]: + if (anothercurly == curly): + break + else: + length = length + len(anothercurly) + parity = (-1)**length + newsequence.factor.multiply(parity) + + # delete the contracted pair from the sequence + del newsequence.sequence[0][0] + del newsequence.sequence[ncurly][noperator] + + # replace any appearance of operator by leftmost + if (leftmost.type == 'general'): + for namplitude in range(len(newsequence.amplitudes)): + amplitude = newsequence.amplitudes[namplitude] + for nindex in range(len(amplitude.indexes)): + index = amplitude.indexes[nindex] + if (leftmost.isidenticalto(index)): + newsequence.amplitudes[namplitude].indexes[nindex] = operator + for nindex in range(len(newsequence.summation.indexes)): + index = newsequence.summation.indexes[nindex] + if (leftmost.isidenticalto(index)): + newsequence.summation.indexes[nindex] = operator + else: + for namplitude in range(len(newsequence.amplitudes)): + amplitude = newsequence.amplitudes[namplitude] + for nindex in range(len(amplitude.indexes)): + index = amplitude.indexes[nindex] + if (operator.isidenticalto(index)): + newsequence.amplitudes[namplitude].indexes[nindex] = leftmost + for nindex in range(len(newsequence.summation.indexes)): + index = newsequence.summation.indexes[nindex] + if (operator.isidenticalto(index)): + newsequence.summation.indexes[nindex] = leftmost + + # cleanup the empty brackets + newsequence.removeemptycurly() + + # add to the result + result.add(newsequence) + + else: + break + + return result + + def performfullcontraction(self): + """Performs full contraction of a given operator sequence and returns a list of tensor contractions""" + + print(self.show()) + print(" ... commencing full operator contraction") + + # result will be a list of tensor contractions (operator sequence objects with empty operator sequence) + result = ListOperatorSequences() + result.add(self) + + # see if already fully contracted + done = self.alreadycontracted() + + # recursive execution of performcontraction() + iteration = 0 + while (not done): + iteration = iteration + 1 + newresult = ListOperatorSequences() + for halfwaycontracted in result.list: + newaddition = halfwaycontracted.performcontraction() + if (newaddition): + newresult.join(newaddition) + newresult.simplifyone() + numberofterms = len(newresult.list) + print(" ... iteration = %d, number of terms = %d" %(iteration, numberofterms)) + done = 1 + for halfwaycontracted in newresult.list: + if (not halfwaycontracted.alreadycontracted()): + done = 0 + result = newresult.duplicate() + + return result + + def hasthesameform(self,another): + """Checks if two operator sequences have the same form for possible consolidation""" + if (not self.summation.hasthesameform(another.summation)): + return 0 + if (len(self.amplitudes) != len(another.amplitudes)): + return 0 + else: + for namplitude in range(len(self.amplitudes)): + if (not self.amplitudes[namplitude].hasthesameform(another.amplitudes[namplitude])): + return 0 + if (len(self.sequence) != len(another.sequence)): + return 0 + else: + for nsequence in range(len(self.sequence)): + nself = 0 + for operator in self.sequence[nsequence]: + if (operator.type == "hole"): + nself = nself + 1 + nanother = 0 + for operator in another.sequence[nsequence]: + if (operator.type == "hole"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + nself = 0 + for operator in self.sequence[nsequence]: + if (operator.type == "particle"): + nself = nself + 1 + nanother = 0 + for operator in another.sequence[nsequence]: + if (operator.type == "particle"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + nself = 0 + for operator in self.sequence[nsequence]: + if (operator.type == "general"): + nself = nself + 1 + nanother = 0 + for operator in another.sequence[nsequence]: + if (operator.type == "general"): + nanother = nanother + 1 + if (nself != nanother): + return 0 + return 1 + + def isidenticalto(self,another): + """Returns true if two operator sequences are identical except for the factor""" + + if (not self.summation.isidenticalto(another.summation)): + return 0 + if (len(self.amplitudes) != len(another.amplitudes)): + return 0 + if (len(self.sequence) != len(another.sequence)): + return 0 + for namplitude in range(len(self.amplitudes)): + if (not self.amplitudes[namplitude].isidenticalto(another.amplitudes[namplitude])): + return 0 + for nsequence in range(len(self.sequence)): + if (len(self.sequence[nsequence]) != len(another.sequence[nsequence])): + return 0 + else: + for noperator in range(len(self.sequence[nsequence])): + if (not self.sequence[nsequence][noperator].isidenticalto(another.sequence[nsequence][noperator])): + return 0 + return 1 + + def has(self,index): + """Checks if a certain index is included in an operator sequence""" + + # see if the index is in summation indexes + for another in self.summation.indexes: + if (another.isidenticalto(index)): + return 1 + + # see if the index is in amplitude indexes + for amplitude in self.amplitudes: + for another in amplitude.indexes: + if (another.isidenticalto(index)): + return 1 + + # see if the index is in the operator sequences + for sequence in self.sequence: + for another in sequence: + if (another.isidenticalto(index)): + return 1 + + # not included + return 0 + + def relabels(self,another): + """Relabels the operator indexes to help consolidate terms""" + + if (not self.hasthesameform(another)): + return another + + else: + + # find a lone index in summation indexes + for index in self.summation.indexes: + if (not another.has(index)): + for anotherindex in another.summation.indexes: + if ((not self.has(anotherindex)) and (index.issimilarto(anotherindex))): + + # at this point, we know that we should relabel anotherindex by index everywhere in another + for nyetanother in range(len(another.summation.indexes)): + yetanother = another.summation.indexes[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.summation.indexes[nyetanother] = copy.deepcopy(index) + + for namplitude in range(len(another.amplitudes)): + amplitude = another.amplitudes[namplitude] + for nyetanother in range(len(amplitude.indexes)): + yetanother = amplitude.indexes[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.amplitudes[namplitude].indexes[nyetanother] = copy.deepcopy(index) + + for nsequence in range(len(another.sequence)): + sequence = another.sequence[nsequence] + for nyetanother in range(len(sequence)): + yetanother = sequence[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.sequence[nsequence][nyetanother] = copy.deepcopy(index) + + return another + + # find a lone index in amplitude indexes + for selfamplitude in self.amplitudes: + for index in selfamplitude.indexes: + if (not another.has(index)): + for anotheramplitude in another.amplitudes: + for anotherindex in anotheramplitude.indexes: + if ((not self.has(anotherindex)) and (index.issimilarto(anotherindex))): + + # at this point, we know that we should relabel anotherindex by index everywhere in another + for nyetanother in range(len(another.summation.indexes)): + yetanother = another.summation.indexes[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.summation.indexes[nyetanother] = copy.deepcopy(index) + + for namplitude in range(len(another.amplitudes)): + amplitude = another.amplitudes[namplitude] + for nyetanother in range(len(amplitude.indexes)): + yetanother = amplitude.indexes[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.amplitudes[namplitude].indexes[nyetanother] = copy.deepcopy(index) + + for nsequence in range(len(another.sequence)): + sequence = another.sequence[nsequence] + for nyetanother in range(len(sequence)): + yetanother = sequence[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.sequence[nsequence][nyetanother] = copy.deepcopy(index) + + return another + + # find a lone index in operator sequences + for selfsequence in self.sequence: + for index in selfsequence: + if (not another.has(index)): + for anothersequence in another.sequence: + for anotherindex in anothersequence: + if ((not self.has(anotherindex)) and (index.issimilarto(anotherindex))): + + # at this point, we know that we should relabel anotherindex by index everywhere in another + for nyetanother in range(len(another.summation.indexes)): + yetanother = another.summation.indexes[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.summation.indexes[nyetanother] = copy.deepcopy(index) + + for namplitude in range(len(another.amplitudes)): + amplitude = another.amplitudes[namplitude] + for nyetanother in range(len(amplitude.indexes)): + yetanother = amplitude.indexes[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.amplitudes[namplitude].indexes[nyetanother] = copy.deepcopy(index) + + for nsequence in range(len(another.sequence)): + sequence = another.sequence[nsequence] + for nyetanother in range(len(sequence)): + yetanother = sequence[nyetanother] + if (yetanother.isidenticalto(anotherindex)): + another.sequence[nsequence][nyetanother] = copy.deepcopy(index) + + return another + + return another + + def fullyrelabels(self,another): + """Relabels the operator indexes to help consolidate terms""" + + if (not self.hasthesameform(another)): + return another + else: + done = 0 + while (not done): + another = self.relabels(another) + done = self.hasnomismatch(another) + + return another + + def hasnomismatch(self,another): + """Returns 1 if there is no index in self that does not exist in another""" + + if (not self.hasthesameform(another)): + return 0 + + nomismatch = 1 + for index in self.summation.indexes: + if (not another.has(index)): + nomismatch = 0 + for selfamplitude in self.amplitudes: + for index in selfamplitude.indexes: + if (not another.has(index)): + nomismatch = 0 + for selfsequence in self.sequence: + for index in selfsequence: + if (not another.has(index)): + nomismatch = 0 + + return nomismatch + + def canmerge(self,another): + """Returns 1 if another operator sequence can be merged to itself""" + + # do they have any index mismatch? + if (not self.hasnomismatch(another)): + return 0 + + # do they have the identical operator sequences? + for nsequence in range(len(self.sequence)): + selfsequence = self.sequence[nsequence] + anothersequence = another.sequence[nsequence] + for noperator in range(len(selfsequence)): + selfoperator = selfsequence[noperator] + anotheroperator = anothersequence[noperator] + if (not selfoperator.isidenticalto(anotheroperator)): + return 0 + + # do they have the summation indexes that do not differ by more than just permutation? + for selfindex in self.summation.indexes: + exist = 0 + for anotherindex in another.summation.indexes: + if (anotherindex.isidenticalto(selfindex)): + exist = 1 + if (not exist): + return 0 + + # do they have the amplitude indexes that do not differ by more than just permutation? + for namplitude in range(len(self.amplitudes)): + selfamplitude = self.amplitudes[namplitude].indexes + anotheramplitude = another.amplitudes[namplitude].indexes + for selfindex in selfamplitude: + exist = 0 + for anotherindex in anotheramplitude: + if (anotherindex.isidenticalto(selfindex)): + exist = 1 + if (not exist): + return 0 + + return 1 + + def merges(self,another): + """Merges another operator sequence to itself when possible""" + + # parity of a permutation can be computed as the product of parities of all pairwise permutations + parity = 1.0 + + # determine the parity for amplitudes + for namplitude in range(len(self.amplitudes)): + selfamplitude = self.amplitudes[namplitude] + anotheramplitude = another.amplitudes[namplitude] + for nselfindexa in range(len(selfamplitude.indexes)): + selfindexa = selfamplitude.indexes[nselfindexa] + for nselfindexb in range(len(selfamplitude.indexes)): + if (nselfindexb <= nselfindexa): + continue + selfindexb = selfamplitude.indexes[nselfindexb] + for nanotherindexa in range(len(anotheramplitude.indexes)): + anotherindexa = anotheramplitude.indexes[nanotherindexa] + if (anotherindexa.isidenticalto(selfindexa)): + for nanotherindexb in range(len(anotheramplitude.indexes)): + anotherindexb = anotheramplitude.indexes[nanotherindexb] + if (anotherindexb.isidenticalto(selfindexb)): + if (nanotherindexb < nanotherindexa): + parity = parity * (-1.0) + + self.factor.add(another.factor, parity) + + return self + + def swapoperators(self,indexa,indexb): + """Swap indexa and indexb everywhere they appear in self""" + + for nindex in range(len(self.summation.indexes)): + index = self.summation.indexes[nindex] + if (index.isidenticalto(indexa)): + self.summation.indexes[nindex] = indexb + elif (index.isidenticalto(indexb)): + self.summation.indexes[nindex] = indexa + + for namplitude in range(len(self.amplitudes)): + amplitude = self.amplitudes[namplitude] + for nindex in range(len(amplitude.indexes)): + index = amplitude.indexes[nindex] + if (index.isidenticalto(indexa)): + self.amplitudes[namplitude].indexes[nindex] = indexb + elif (index.isidenticalto(indexb)): + self.amplitudes[namplitude].indexes[nindex] = indexa + + for nsequence in range(len(self.sequence)): + sequence = self.sequence[nsequence] + for nindex in range(len(sequence)): + index = sequence[nindex] + if (index.isidenticalto(indexa)): + self.sequence[nsequence][nindex] = indexb + elif (index.isidenticalto(indexb)): + self.sequence[nsequence][nindex] = indexa + + return self + + def swapamplitudes(self,namplitudea,namplitudeb): + """Swap two amplitudes in self""" + + swap = copy.deepcopy(self.amplitudes[namplitudea]) + self.amplitudes[namplitudea] = copy.deepcopy(self.amplitudes[namplitudeb]) + self.amplitudes[namplitudeb] = copy.deepcopy(swap) + + return self + + def targetindexpermutation(self): + """Returns a list of all possible permutations and redundancy of target indexes of self""" + + # generate a target tensor + super = [] + sub = [] + for tensor in self.amplitudes: + for nindex in range(len(tensor.indexes)/2): + index = tensor.indexes[nindex] + common = 0 + if (self.summation): + for another in self.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + super.append(tensor.indexes[nindex]) + for nindex in range(len(tensor.indexes)/2,len(tensor.indexes)): + index = tensor.indexes[nindex] + common = 0 + if (self.summation): + for another in self.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + sub.append(tensor.indexes[nindex]) + + # permutation + result = ListOperatorSequences() + result.add(self.duplicate()) + for nsupera in range(len(super)-1): + result = result.targetsuperpermutation(nsupera) + for nsuba in range(len(sub)-1): + result = result.targetsubpermutation(nsuba) + for operatorsequence in result.list: + newsuper = [] + newsub = [] + for tensor in operatorsequence.amplitudes: + for nindex in range(len(tensor.indexes)/2): + index = tensor.indexes[nindex] + common = 0 + if (operatorsequence.summation): + for another in operatorsequence.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + newsuper.append(tensor.indexes[nindex]) + for nindex in range(len(tensor.indexes)/2,len(tensor.indexes)): + index = tensor.indexes[nindex] + common = 0 + if (operatorsequence.summation): + for another in operatorsequence.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + newsub.append(tensor.indexes[nindex]) + for ncoeff in range(len(operatorsequence.factor.coefficients)): + operatorsequence.factor.coefficients[ncoeff] = self.factor.coefficients[ncoeff] + newpermutation = newsuper + newsub + super + sub + if (operatorsequence.factor.permutations[ncoeff] == []): + operatorsequence.factor.permutations[ncoeff] = newpermutation + else: + operatorsequence.factor.permutations[ncoeff] = combinepermutations(newpermutation, operatorsequence.factor.permutations[ncoeff]) + return result + + def canonicalize(self): + """Reorder amplitudes and common indexes in the canonical order""" + # In canonical order, amplitudes are ordered in alphabetical then size-ascending order. + # Then same amplitudes are ordered in ascending order in target index labels. + # Then all common indexes (that are summation indexes) are renamed in the ascending order. + + another = self.duplicate() + + # reorder amplitudes + done = 0 + while (not done): + done = 1 + for namplitudea in range(len(another.amplitudes)): + for namplitudeb in range(len(another.amplitudes)): + if (namplitudea >= namplitudeb): + continue + amplitudea = another.amplitudes[namplitudea] + amplitudeb = another.amplitudes[namplitudeb] + if (amplitudea.isgreaterthan(amplitudeb,another)): + another.swapamplitudes(namplitudea,namplitudeb) + done = 0 + + # reorder indexes + for namplitude in range(len(another.amplitudes)): + amplitude = another.amplitudes[namplitude] + result = amplitude.canonicalize(another) + another.amplitudes[namplitude] = copy.deepcopy(result[0]) + parity = result[1] + another.factor.multiply(parity) + + # relabel summation indexes in the order of appearance + labelsinuse = [] + for amplitude in another.amplitudes: + for operator in amplitude.indexes: + if (not another.summation.hastheindex(operator)): + labelsinuse.append(operator.index) + for sequence in another.sequence: + for operator in sequence: + if (not another.summation.hastheindex(operator)): + labelsinuse.append(operator.index) + oldlabels = [] + newlabels = [] + newlabel = 0 + for amplitude in another.amplitudes: + for operator in amplitude.indexes: + if (another.summation.hastheindex(operator)): + if (operator.index not in oldlabels): + oldlabels.append(operator.index) + newlabel = newlabel + 1 + while (newlabel in labelsinuse): + newlabel = newlabel + 1 + newlabels.append(newlabel) + for operator in another.summation.indexes: + if (operator.index in oldlabels): + operator.index = newlabels[oldlabels.index(operator.index)] + for amplitude in another.amplitudes: + for operator in amplitude.indexes: + if (operator.index in oldlabels): + operator.index = newlabels[oldlabels.index(operator.index)] + for sequence in another.sequence: + for operator in sequence: + if (operator.index in oldlabels): + operator.index = newlabels[oldlabels.index(operator.index)] + + # reorder summation indexes + for nindexa in range(len(another.summation.indexes)): + indexa = another.summation.indexes[nindexa] + for nindexb in range(len(another.summation.indexes)): + indexb = another.summation.indexes[nindexb] + if (nindexa <= nindexb): + continue + if (indexa.index < indexb.index): + swap = another.summation.indexes[nindexa] + another.summation.indexes[nindexa] = copy.deepcopy(another.summation.indexes[nindexb]) + another.summation.indexes[nindexb] = copy.deepcopy(swap) + + return another + + def isacycliccontraction(self): + """Returns 1 if self is a cyclic contraction""" + ncontractions = 0 + for namplitudea in range(len(self.amplitudes)): + for namplitudeb in range(len(self.amplitudes)): + if (namplitudea > namplitudeb): + amplitudea = self.amplitudes[namplitudea] + amplitudeb = self.amplitudes[namplitudeb] + for operator in self.summation.indexes: + if (operator.isin(amplitudea.indexes) and operator.isin(amplitudeb.indexes)): + ncontractions = ncontractions + 1 + break + if (ncontractions > len(self.amplitudes) - 1): + return 1 + else: + return 0 + + def isdisconnected(self,withrespectto=[]): + """Returns 1 if disconnected; if (withrespectto) connectivity among the given amplitude types is tested""" + + if (self.alreadycontracted()): + + # make a connectedness table + connectedness = [0]*len(self.amplitudes) + connectedness[0] = 1 + for iteration in range(len(self.amplitudes)): + for namplitudea in range(len(self.amplitudes)): + if (connectedness[namplitudea] == 1): + amplitudea = self.amplitudes[namplitudea] + if ((withrespectto) and (amplitudea.type not in withrespectto)): + continue + for namplitudeb in range(len(self.amplitudes)): + if (connectedness[namplitudeb] == 0): + amplitudeb = self.amplitudes[namplitudeb] + if ((withrespectto) and (amplitudeb.type not in withrespectto)): + continue + + # see if they have at least one common index + exist = 0 + for indexa in amplitudea.indexes: + for indexb in amplitudeb.indexes: + if (indexa.isidenticalto(indexb)): + exist = 1 + if (exist): + connectedness[namplitudeb] = 1 + + if (0 not in connectedness): + # connected! + return 0 + else: + if (withrespectto): + for namplitudea in range(len(self.amplitudes)): + amplitudea = self.amplitudes[namplitudea] + if (amplitudea.type in withrespectto): + if (connectedness[namplitudea] == 0): + return 1 + return 0 + + else: + return 1 + + else: + return 0 + + def isunlinked(self): + """Returns 1 if unlinked""" + + if (not self.isdisconnected()): + return 0 + + for seed in range(len(self.amplitudes)): + # make a connectedness table + connectedness = [0]*len(self.amplitudes) + connectedness[seed] = 1 + for iteration in range(len(self.amplitudes)): + for namplitudea in range(len(self.amplitudes)): + if (connectedness[namplitudea] == 1): + amplitudea = self.amplitudes[namplitudea] + for namplitudeb in range(len(self.amplitudes)): + if (connectedness[namplitudeb] == 0): + amplitudeb = self.amplitudes[namplitudeb] + + # see if they have at least one common index + exist = 0 + for indexa in amplitudea.indexes: + for indexb in amplitudeb.indexes: + if (indexa.isidenticalto(indexb)): + exist = 1 + if (exist): + connectedness[namplitudeb] = 1 + + if (0 in connectedness): + # disconnected + closed = 1 + for namplitudeb in range(len(self.amplitudes)): + amplitudeb = self.amplitudes[namplitudeb] + if (connectedness[namplitudeb] == 1): + for indexa in amplitudeb.indexes: + if (not self.summation.hastheindex(indexa)): + closed = 0 + if (closed): + # disconnected & closed = unlinked + return 1 + + return 0 + + def iszero(self): + """True if the numerical factor is computationally zero""" + threshold = 1.0e-12 + zero = 1 + for coefficient in self.factor.coefficients: + if (abs(coefficient) > threshold): + zero = 0 + return zero + +class ListOperatorSequences: + + def __init__(self): + """Creates a list of operator sequence objects""" + self.list = [] + + def __str__(self): + """Prints the sequences of operator contractions""" + print("") + for line in self.show(): + print(line) + return "" + + def show(self): + """Returns a human-friendly string of the content""" + show = [] + for operatorsequence in self.list: + if (operatorsequence == "deleted"): + show.append("deleted") + else: + show.append(operatorsequence.show()) + return show + + def tex(self): + """Returns a LaTeX string of the content""" + show = [] + for noperatorsequence in range(len(self.list)): + operatorsequence = self.list[noperatorsequence] + if (operatorsequence != "deleted"): + if (noperatorsequence == 0): + show.append("\\begin{eqnarray}") + show.append(string.join(["&&",operatorsequence.tex(),"\\nonumber\\\\"],"")) + elif (noperatorsequence == len(self.list)-1): + show.append(string.join(["&&",operatorsequence.tex(),"\\nonumber"],"")) + show.append("\\end{eqnarray}") + else: + show.append(string.join(["&&",operatorsequence.tex(),"\\nonumber\\\\"],"")) + return show + + def duplicate(self): + """Makes a copy of itself""" + duplicate = ListOperatorSequences() + for operatorsequence in self.list: + duplicate.list.append(operatorsequence.duplicate()) + return duplicate + + def writetofile(self,filename): + """Writes the output to a given file""" + file = open(filename,"w") + for operatorsequence in self.list: + file.write(operatorsequence.show()) + file.write("\n") + + def appendtofile(self,filename): + """Writes the output to a given file""" + file = open(filename,"a") + for operatorsequence in self.list: + file.write(operatorsequence.show()) + file.write("\n") + + def add(self,newoperatorsequence): + """Adds a new operator sequence member to the list""" + self.list.append(newoperatorsequence) + + def join(self,another): + """Joins two list operator sequences""" + for operatorsequence in another.list: + self.list.append(operatorsequence) + + def performcontraction(self): + """Perform a contraction of the left-most operator""" + + # result will be a list of new operator sequence objects + result = ListOperatorSequences() + + # loop over operator sequences + for operatorsequence in self.list: + + # call performcontraction() + result.join(operatorsequence.performcontraction()) + + return result + + def simplifythreesub(self,verbose=0): + """Simplify the list by consolidating operator sequences using permutation of operators""" + + if (len(self.list) == 1): + return self + + # pick up a pair of operator sequences + for nsequencea in range(len(self.list)): +# if (verbose): +# print('processing ',nsequencea,' / ',range(len(self.list))) + sequencea = self.list[nsequencea] + for nsequenceb in range(len(self.list)): + sequenceb = self.list[nsequenceb] + if (nsequenceb <= nsequencea): + continue + if (sequencea.hasthesameform(sequenceb)): + sequencec = sequencea.fullyrelabels(sequenceb) + if (sequencea.canmerge(sequencec)): + self.add(sequencea.merges(sequencec)) + # It is extremely important that the following two statements are executed in this order + del self.list[nsequenceb] + del self.list[nsequencea] + return self + elif (sequencea.hasnomismatch(sequencec)): + permutation = ListOperatorSequences() + permutation.add(sequencec) + # permutation of tensors + for namplitude in range(len(sequencec.amplitudes)): + permutation = permutation.amplitudepermutation(namplitude) + for sequenced in permutation.list: + if (sequencea.canmerge(sequenced)): + self.add(sequencea.merges(sequenced)) + # It is extremely important that the following two statements are executed in this order + del self.list[nsequenceb] + del self.list[nsequencea] + return self + # permutation of summation indexes + for noperator in range(len(sequencec.summation.indexes)): + permutation = permutation.operatorpermutation(noperator) + for sequenced in permutation.list: + if (sequencea.canmerge(sequenced)): + self.add(sequencea.merges(sequenced)) + # It is extremely important that the following two statements are executed in this order + del self.list[nsequenceb] + del self.list[nsequencea] + return self + + return self + + def simplifyfoursub(self,quick=0): + """Identify the permutation symmetry among the target indexes""" + + if (len(self.list) == 1): + return self + + # pick up a pair of operator sequences + for nsequencea in range(len(self.list)): + sequencea = self.list[nsequencea] + for nsequenceb in range(len(self.list)): + sequenceb = self.list[nsequenceb] + if (nsequenceb <= nsequencea): + continue + if (sequencea.hasthesameform(sequenceb)): + sequencec = sequencea.fullyrelabels(sequenceb) + if (sequencea.hasnomismatch(sequencec)): + permutation = sequencec.targetindexpermutation() + # permutation of target indexes + for sequenced in permutation.list: + if (sequencea.canmerge(sequenced)): + self.add(sequencea.merges(sequenced)) + # Important that the following two statements are executed in this order + del self.list[nsequenceb] + del self.list[nsequencea] + return self + if (quick): + continue + seed = ListOperatorSequences() + seed.add(sequencec) + # permutation of tensors + for namplitude in range(len(sequencec.amplitudes)): + seed = seed.amplitudepermutation(namplitude) + for noperator in range(len(sequencec.summation.indexes)): + seed = seed.operatorpermutation(noperator) + permutation = ListOperatorSequences() + for sequenced in seed.list: + permutation.join(sequenced.targetindexpermutation()) + for sequenced in permutation.list: + if (sequencea.canmerge(sequenced)): + self.add(sequencea.merges(sequenced)) + # It is extremely important that the following two statements are executed in this order + del self.list[nsequenceb] + del self.list[nsequencea] + return self + + return self + + def simplify(self,verbose=0): + """Call simplyone through four""" + #self.simplifyone(1) + if (self.containscycliccontractions()): + print(" ! Warning! a cyclic contraction is found") +# self.simplifythree(verbose) + self.simplifytwo(verbose) + # the followings do not seem to affect the result, yet it costs enormous memory & time + # self.simplifyfour(1) + self = copy.deepcopy(self.deletezero()) + return self + + def simplifyone(self,verbose=0): + """Consolidate the identical operator sequences""" + if (len(self.list) == 0): + return self + if (verbose): + print(" ... canonicalizing the expressions") + self = self.canonicalize() + if (len(self.list) == 1): + return self + if (verbose): + print(" ... consolidating terms") + originallength = len(self.list) + # pick up a pair of operator sequences + for nsequencea in range(len(self.list)): + if (verbose): + if ((nsequencea/100)*100 == nsequencea): + print("simplifying:",nsequencea,"/",len(self.list)) + sequencea = self.list[nsequencea] + if (sequencea == "deleted"): + continue + for nsequenceb in range(len(self.list)): + sequenceb = self.list[nsequenceb] + if (nsequenceb <= nsequencea): + continue + if (sequenceb == "deleted"): + continue + if (sequencea.isidenticalto(sequenceb)): + sequencea.factor.add(sequenceb.factor,1) + self.list[nsequencea] = copy.deepcopy(sequencea) + self.list[nsequenceb] = "deleted" + numberofdeleted = self.list.count("deleted") + for dummy in range(numberofdeleted): + self.list.remove("deleted") + if (verbose): + print(" ... %d terms have been consolidated" %(originallength - len(self.list))) + print(" ... number of terms = %d" %(len(self.list))) + return self + + def simplifytwo(self,verbose=0): + """Identify the permutation symmetries of target indexes""" + if (len(self.list) == 0): + return self + self = self.canonicalize() + if (len(self.list) == 1): + return self + print(" ... identifying permutation symmetry among target indexes") + originallength = len(self.list) + # pick up a pair of operator sequences + for nsequencea in range(len(self.list)): + if (verbose): + if ((nsequencea/10)*10 == nsequencea): + print("permutation-simplifying:",nsequencea,"/",len(self.list)) + sequencea = self.list[nsequencea] + if (sequencea == "deleted"): + continue + for nsequenceb in range(len(self.list)): + if (nsequenceb <= nsequencea): + continue + sequenceb = self.list[nsequenceb] + if (sequenceb == "deleted"): + continue + if (sequencea.hasthesameform(sequenceb)): + permutation = sequenceb.targetindexpermutation() + permutation = permutation.canonicalize() + for sequencec in permutation.list: + if (sequencea.isidenticalto(sequencec)): + sequencea.factor.add(sequencec.factor,1) + self.list[nsequencea] = copy.deepcopy(sequencea) + self.list[nsequenceb] = "deleted" + break + numberofdeleted = self.list.count("deleted") + for dummy in range(numberofdeleted): + self.list.remove("deleted") + print(" ... %d terms have been consolidated" %(originallength - len(self.list))) + print(" ... number of terms = %d" %(len(self.list))) + return self + + def simplifythree(self,verbose=0): + """Aggressively consolidate identical terms""" + if (len(self.list) == 0): + return self + elif (len(self.list) == 1): + return self + if (verbose): + print(" ... aggressively consolidating terms") + done = 0 + iteration = 0 + originallength = len(self.list) + while (not done): + iteration = iteration + 1 + if (verbose): + print('iteration ',iteration,' number of terms ',len(self.list)) + beforesimplify = len(self.list) + self = self.simplifythreesub(verbose) + if (len(self.list) < beforesimplify): + done = 0 + else: + done = 1 + print(" ... %d terms have been consolidated" %(originallength - len(self.list))) + print(" ... number of terms = %d" %(len(self.list))) + return self + + def simplifyfour(self,verbose=0): + """Aggressively identify the permutation symmetries of target indexes""" + if (len(self.list) == 0): + return self + elif (len(self.list) == 1): + return self + if (verbose): + print(" ... aggressively identifying permutation symmetry among target indexes") + originallength = len(self.list) + # quick merge to reduce the number of terms + done = 0 + iteration = 0 + while (not done): + iteration = iteration + 1 + beforesimplify = len(self.list) + self = self.simplifyfoursub(1) + if (len(self.list) < beforesimplify): + done = 0 + else: + done = 1 + # more exhaustive merge + done = 0 + iteration = 0 + while (not done): + iteration = iteration + 1 + beforesimplify = len(self.list) + self = self.simplifyfoursub(0) + if (len(self.list) < beforesimplify): + done = 0 + else: + done = 1 + if (originallength - len(self.list) > 0): + print(" ... ***** warning *****") + print(" ... %d terms have been consolidated" %(originallength - len(self.list))) + print(" ... number of terms = %d" %(len(self.list))) + return self + + def performfullcontraction(self): + """Performs full contraction of a list of operator sequences and returns a list of tensor contractions""" + + # result will be a list of tensor contractions (operator sequence objects with empty operator sequence) + self = self.simplifyone() + result = ListOperatorSequences() + + # loop over operator sequences + for operatorsequence in self.list: + + # call performcontraction() + result.join(operatorsequence.performfullcontraction()) + + return result + + def operatorpermutation(self,noperatora=0): + """Return all possible permutation of operators in self""" + + result = ListOperatorSequences() + + for operatorsequence in self.list: + result.add(operatorsequence) + if (operatorsequence.summation.indexes): + operatora = operatorsequence.summation.indexes[noperatora] + for noperatorb in range(len(operatorsequence.summation.indexes)): + if (noperatorb <= noperatora): + continue + operatorb = operatorsequence.summation.indexes[noperatorb] + if (not operatora.issimilarto(operatorb)): + continue + permutation = operatorsequence.duplicate() + permutation.swapoperators(operatora,operatorb) + result.add(permutation) + + return result + + def amplitudepermutation(self,namplitudea=0): + """Return all possible permutation of amplitude in self""" + + result = ListOperatorSequences() + + for operatorsequence in self.list: + result.add(operatorsequence) + amplitudea = operatorsequence.amplitudes[namplitudea] + for namplitudeb in range(len(operatorsequence.amplitudes)): + if (namplitudeb <= namplitudea): + continue + amplitudeb = operatorsequence.amplitudes[namplitudeb] + if (amplitudea.type != amplitudeb.type): + continue + permutation = operatorsequence.duplicate() + permutation.swapamplitudes(namplitudea,namplitudeb) + result.add(permutation) + + return result + + def targetsuperpermutation(self,nsupera=0): + """Return all possible permutation of target super indexes in self""" + + result = ListOperatorSequences() + + for operatorsequence in self.list: + + super = [] + sub = [] + for tensor in operatorsequence.amplitudes: + for nindex in range(len(tensor.indexes)/2): + index = tensor.indexes[nindex] + common = 0 + if (operatorsequence.summation): + for another in operatorsequence.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + super.append(tensor.indexes[nindex]) + for nindex in range(len(tensor.indexes)/2,len(tensor.indexes)): + index = tensor.indexes[nindex] + common = 0 + if (operatorsequence.summation): + for another in operatorsequence.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + sub.append(tensor.indexes[nindex]) + + result.add(operatorsequence) + supera = super[nsupera] + for nsuperb in range(len(super)): + if (nsuperb <= nsupera): + continue + superb = super[nsuperb] + permutation = operatorsequence.duplicate() + permutation.swapoperators(supera,superb) + result.add(permutation) + + return result + + def targetsubpermutation(self,nsuba=0): + """Return all possible permutation of target sub indexes in self""" + + result = ListOperatorSequences() + + for operatorsequence in self.list: + + super = [] + sub = [] + for tensor in operatorsequence.amplitudes: + for nindex in range(len(tensor.indexes)/2): + index = tensor.indexes[nindex] + common = 0 + if (operatorsequence.summation): + for another in operatorsequence.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + super.append(tensor.indexes[nindex]) + for nindex in range(len(tensor.indexes)/2,len(tensor.indexes)): + index = tensor.indexes[nindex] + common = 0 + if (operatorsequence.summation): + for another in operatorsequence.summation.indexes: + if (index.isidenticalto(another)): + common = 1 + if (not common): + sub.append(tensor.indexes[nindex]) + + result.add(operatorsequence) + suba = sub[nsuba] + for nsubb in range(len(sub)): + if (nsubb <= nsuba): + continue + subb = sub[nsubb] + permutation = operatorsequence.duplicate() + permutation.swapoperators(suba,subb) + result.add(permutation) + + return result + + def canonicalize(self): + """Reorder amplitudes and common indexes in the canonical order""" + + for noperatorsequence in range(len(self.list)): + operatorsequence = self.list[noperatorsequence] + self.list[noperatorsequence] = operatorsequence.canonicalize() + return self + + def deletedisconnected(self,withrespectto=[]): + """Deletes disconnected terms""" + + result = ListOperatorSequences() + + originallength = len(self.list) + + # for a fully contracted sequence ... + for noperatorsequence in range(len(self.list)): + operatorsequence = self.list[noperatorsequence] + if (not operatorsequence.isdisconnected(withrespectto)): + result.add(operatorsequence) + + newlength = len(result.list) + + print(" ... %d disconnected terms have been deleted" %(originallength - newlength)) + + return result + + def deleteunlinked(self): + """Deletes unlinked terms""" + + result = ListOperatorSequences() + + originallength = len(self.list) + + # for a fully contracted sequence ... + for noperatorsequence in range(len(self.list)): + operatorsequence = self.list[noperatorsequence] + if (not operatorsequence.isunlinked()): + result.add(operatorsequence) + + newlength = len(result.list) + + print(" ... %d unlinked terms have been deleted" %(originallength - newlength)) + + return result + + def containscycliccontractions(self): + """Returns 1 if self contains a cyclic contraction""" + for operatorsequence in self.list: + if (operatorsequence.isacycliccontraction()): + return 1 + return 0 + + def relabelamplitudes(self,old,new): + """Relabels amplitude""" + for noperatorsequence in range(len(self.list)): + operatorsequence = self.list[noperatorsequence] + for namplitude in range(len(operatorsequence.amplitudes)): + amplitude = operatorsequence.amplitudes[namplitude] + if (amplitude.type == old): + self.list[noperatorsequence].amplitudes[namplitude].type = copy.deepcopy(new) + return self + + def deletezero(self): + """Deletes computationally zero terms""" + + result = ListOperatorSequences() + + originallength = len(self.list) + + # for a fully contracted sequence ... + for noperatorsequence in range(len(self.list)): + operatorsequence = self.list[noperatorsequence] + if (not operatorsequence.iszero()): + result.add(operatorsequence) + + newlength = len(result.list) + + if (originallength != newlength): + print(" !!! WARNING !!! %d computationally zero terms have been deleted" %(originallength - newlength)) + + return result diff --git a/src/tce/splitfiles.py b/src/tce/splitfiles.py new file mode 100644 index 0000000..75613a3 --- /dev/null +++ b/src/tce/splitfiles.py @@ -0,0 +1,32 @@ +#!/usr/bin/env python3 +# Usage: python splitfiles.py < inputfile.F +# (c) All rights reserved by Battelle & Pacific Northwest Nat'l Lab (2002) +# $Id$ + +import string +import copy +import sys + +source = sys.stdin.readlines() + +if (not source): + print("Usage: python splitfiles.py < inputfile.F") + +nfiles = 0 +for line in source: + if (string.find(line,"SUBROUTINE") != -1): + if (nfiles): + file = open(filename+".F","w") + for newline in filecontent: + file.write(newline) + filename = string.split(line[string.find(line,"SUBROUTINE")+11:],"(")[0] + print(filename+".o\\") + nfiles = nfiles + 1 + filecontent = [line] + else: + filecontent.append(line) +# don't forget to dump the last subroutine +file = open(filename+".F","w") +for newline in filecontent: + file.write(newline) +print("Number of files generated:",nfiles) diff --git a/src/util/errquit.h b/src/util/errquit.h new file mode 100644 index 0000000..9c86292 --- /dev/null +++ b/src/util/errquit.h @@ -0,0 +1,33 @@ +// UERR - Not yet assigned to a category +// UNKNOWN_ERR - Not yet assigned to a category +// MEM_ERROR - Generic Memory error +// RTDB_ERR - Error in the Runtime Database +// INPUT_ERR - Error resulting from inproper user input +// CAPMIS_ERR - Features that have not been implemented yet +// BASIS_ERR - Error related to basis set +// GEOM_ERR - Error related to geometry +// MA_ERR - local memory error +// GA_ERR - global memory error +// INT_ERR - error related to integrals +// DISK_ERR - error in reading or writing from disk +// CALC_ERR - calculation failed to converge +// FMM_ERR - +// STACK_ERR - error in MA stack +// HEAP_ERR - error in MA heap +const int UERR = 0; +const int UNKNOWN_ERR = 0; +const int MEM_ERR = 10; +const int STACK_ERR = 11; +const int HEAP_ERR = 12; +const int RTDB_ERR = 20; +const int INPUT_ERR = 30; +const int CAPMIS_ERR = 40; +const int BASIS_ERR = 50; +const int GEOM_ERR = 60; +const int GA_ERR = 70; +const int MA_ERR = 80; +const int INT_ERR = 90; +const int DISK_ERR = 100; +const int CALC_ERR = 110; +const int FMM_ERR = 120; +// $Id$ From 56ec4c5abee074eaa48cba32f53db74b706156a0 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Tue, 1 Nov 2022 13:30:14 -0700 Subject: [PATCH 03/11] add README --- README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..e69de29 From d611aff5430280090df2c00770c4b985248c68c1 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Wed, 14 Jun 2023 11:44:26 -0700 Subject: [PATCH 04/11] Added .gitignore file --- .gitignore | 110 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 110 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ebf6d6b --- /dev/null +++ b/.gitignore @@ -0,0 +1,110 @@ + +# Created by https://www.gitignore.io/api/c,cuda,linux,windows + +### C ### +# Prerequisites +*.d + +# Object files +*.o +*.ko +*.obj +*.elf + +# Linker output +*.ilk +*.map +*.exp + +# Precompiled Headers +*.gch +*.pch + +# Libraries +*.lib +*.a +*.la +*.lo + +# Shared objects (inc. Windows DLLs) +*.dll +*.so +*.so.* +*.dylib + +# Executables +#*.exe +#*.out # output files +*.app +*.i*86 +*.x86_64 +*.hex + +# Debug files +*.dSYM/ +*.su +*.idb +*.pdb + +# Kernel Module Compile Results +*.mod* +*.cmd +.tmp_versions/ +modules.order +Module.symvers +Mkfile.old +dkms.conf + +### CUDA ### +*.i +*.ii +*.gpu +*.ptx +*.cubin +*.fatbin + +### Linux ### +*~ + +### VS Code ### +.vscode + +# temporary files which can be created if a process still has a handle open of a deleted file +.fuse_hidden* + +# KDE directory preferences +.directory + +# Linux trash folder which might appear on any partition or disk +.Trash-* + +# .nfs files are created when an open file is removed but is still being accessed +.nfs* + +### Windows ### +# Windows thumbnail cache files +Thumbs.db +ehthumbs.db +ehthumbs_vista.db + +# Folder config file +Desktop.ini + +# Recycle Bin used on file shares +$RECYCLE.BIN/ + +# Windows Installer files +*.cab +*.msi +*.msm +*.msp + +# Windows shortcuts +*.lnk + +# End of https://www.gitignore.io/api/c,cuda,linux,windows + +# debris created in nwchem compilations +include_stamp +dependencies +# End of debris created in nwchem compilations \ No newline at end of file From f6c3a71f6ded99b3b8da939c3878d891dead554b Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Wed, 14 Jun 2023 11:44:49 -0700 Subject: [PATCH 05/11] Added data files --- src/data/amber_q/ABE.frg | 45 + src/data/amber_q/BNZ.frg | 23 + src/data/amber_q/BTH.frg | 28 + src/data/amber_q/BTH.sgm | 129 + src/data/amber_q/BTO.frg | 26 + src/data/amber_q/BTO.sgm | 115 + src/data/amber_q/BUT.frg | 30 + src/data/amber_q/BUT.sgm | 145 + src/data/amber_q/CA.frg | 5 + src/data/amber_q/CTR.frg | 13 + src/data/amber_q/Ca.sgm | 7 + src/data/amber_q/DTT.frg | 92 + src/data/amber_q/EAM.frg | 24 + src/data/amber_q/FUC.sgm | 339 ++ src/data/amber_q/G31.frg | 33 + src/data/amber_q/G61.frg | 33 + src/data/amber_q/G64.frg | 32 + src/data/amber_q/GA1.frg | 49 + src/data/amber_q/GA2.frg | 47 + src/data/amber_q/GA3.frg | 65 + src/data/amber_q/GA3.sgm | 383 +++ src/data/amber_q/GAL.frg | 47 + src/data/amber_q/GAO.frg | 45 + src/data/amber_q/GC1.frg | 45 + src/data/amber_q/GC2.frg | 41 + src/data/amber_q/GC2.sgm | 229 ++ src/data/amber_q/GC3.sgm | 275 ++ src/data/amber_q/GCN.frg | 61 + src/data/amber_q/GDP.frg | 95 + src/data/amber_q/GL1.frg | 45 + src/data/amber_q/GL2.frg | 45 + src/data/amber_q/GL3.frg | 49 + src/data/amber_q/GL4.frg | 49 + src/data/amber_q/GL4.sgm | 275 ++ src/data/amber_q/GL5.frg | 51 + src/data/amber_q/GL5.sgm | 287 ++ src/data/amber_q/GL6.frg | 49 + src/data/amber_q/GL6.sgm | 275 ++ src/data/amber_q/GL7.frg | 51 + src/data/amber_q/GL7.sgm | 287 ++ src/data/amber_q/GL8.sgm | 263 ++ src/data/amber_q/GLT.sgm | 287 ++ src/data/amber_q/GNP.frg | 105 + src/data/amber_q/GTL.sgm | 401 +++ src/data/amber_q/GTP.frg | 103 + src/data/amber_q/HDH.frg | 34 + src/data/amber_q/HDH.sgm | 169 + src/data/amber_q/HDO.frg | 32 + src/data/amber_q/HDO.sgm | 157 + src/data/amber_q/HED.sgm | 161 + src/data/amber_q/HEM.frg | 156 + src/data/amber_q/HEP.frg | 50 + src/data/amber_q/HEP.sgm | 271 ++ src/data/amber_q/HP1.frg | 51 + src/data/amber_q/HP2.frg | 49 + src/data/amber_q/HP3.frg | 57 + src/data/amber_q/HP4.frg | 47 + src/data/amber_q/HP4.sgm | 245 ++ src/data/amber_q/HP5.frg | 65 + src/data/amber_q/HP5.sgm | 373 +++ src/data/amber_q/HPD.frg | 41 + src/data/amber_q/HXO.frg | 38 + src/data/amber_q/IPS.frg | 16 + src/data/amber_q/KD1.frg | 57 + src/data/amber_q/KD2.frg | 59 + src/data/amber_q/KD3.frg | 59 + src/data/amber_q/KD4.frg | 55 + src/data/amber_q/KD4.sgm | 307 ++ src/data/amber_q/KD5.frg | 61 + src/data/amber_q/KD5.sgm | 353 ++ src/data/amber_q/KDN.frg | 43 + src/data/amber_q/LCX.frg | 61 + src/data/amber_q/LPO.sgm | 177 + src/data/amber_q/MA2.sgm | 401 +++ src/data/amber_q/MA3.sgm | 411 +++ src/data/amber_q/MA4.sgm | 423 +++ src/data/amber_q/MAN.frg | 45 + src/data/amber_q/NH4.frg | 16 + src/data/amber_q/NTR.frg | 13 + src/data/amber_q/Na.sgm | 7 + src/data/amber_q/O4P.frg | 14 + src/data/amber_q/PET.frg | 38 + src/data/amber_q/PET.sgm | 187 ++ src/data/amber_q/PNT.frg | 34 + src/data/amber_q/PO4.frg | 14 + src/data/amber_q/PO4.sgm | 35 + src/data/amber_q/PPO.frg | 22 + src/data/amber_q/RH2.frg | 47 + src/data/amber_q/RH2.sgm | 263 ++ src/data/amber_q/RH3.sgm | 263 ++ src/data/amber_q/RHA.frg | 45 + src/data/amber_q/SEP.frg | 30 + src/data/amber_q/SO4.frg | 16 + src/data/amber_q/TPO.frg | 41 + src/data/amber_q/amber.par | 219 ++ src/data/amber_q/coc.frg | 14 + src/data/amber_q/etl.frg | 16 + src/data/amber_q/ions.par | 145 + src/data/amber_q/lps_Pa/BTH.frg | 28 + src/data/amber_q/lps_Pa/BTH.sgm | 129 + src/data/amber_q/lps_Pa/BTO.frg | 26 + src/data/amber_q/lps_Pa/BTO.sgm | 115 + src/data/amber_q/lps_Pa/BUT.frg | 30 + src/data/amber_q/lps_Pa/BUT.sgm | 145 + src/data/amber_q/lps_Pa/GA3.frg | 65 + src/data/amber_q/lps_Pa/GA3.sgm | 383 +++ src/data/amber_q/lps_Pa/GC3.sgm | 275 ++ src/data/amber_q/lps_Pa/GL4.frg | 49 + src/data/amber_q/lps_Pa/GL4.sgm | 275 ++ src/data/amber_q/lps_Pa/GL5.frg | 51 + src/data/amber_q/lps_Pa/GL5.sgm | 287 ++ src/data/amber_q/lps_Pa/GL6.frg | 49 + src/data/amber_q/lps_Pa/GL6.sgm | 275 ++ src/data/amber_q/lps_Pa/GL7.frg | 51 + src/data/amber_q/lps_Pa/GL7.sgm | 287 ++ src/data/amber_q/lps_Pa/HDH.frg | 34 + src/data/amber_q/lps_Pa/HDH.sgm | 169 + src/data/amber_q/lps_Pa/HDO.frg | 32 + src/data/amber_q/lps_Pa/HDO.sgm | 157 + src/data/amber_q/lps_Pa/HEP.frg | 50 + src/data/amber_q/lps_Pa/HEP.sgm | 271 ++ src/data/amber_q/lps_Pa/HP4.frg | 47 + src/data/amber_q/lps_Pa/HP4.sgm | 245 ++ src/data/amber_q/lps_Pa/HP5.frg | 65 + src/data/amber_q/lps_Pa/HP5.sgm | 373 +++ src/data/amber_q/lps_Pa/KD4.frg | 55 + src/data/amber_q/lps_Pa/KD4.sgm | 307 ++ src/data/amber_q/lps_Pa/KD5.frg | 61 + src/data/amber_q/lps_Pa/KD5.sgm | 353 ++ src/data/amber_q/lps_Pa/PET.frg | 38 + src/data/amber_q/lps_Pa/PET.sgm | 187 ++ src/data/amber_q/lps_Pa/PO4.frg | 14 + src/data/amber_q/lps_Pa/PO4.sgm | 35 + src/data/amber_q/lps_Pa/RH2.frg | 47 + src/data/amber_q/lps_Pa/RH2.sgm | 263 ++ src/data/amber_q/lps_ec/BU1.frg | 34 + src/data/amber_q/lps_ec/BU2.frg | 32 + src/data/amber_q/lps_ec/GA1.frg | 55 + src/data/amber_q/lps_ec/GL1.frg | 47 + src/data/amber_q/lps_ec/GL2.frg | 51 + src/data/amber_q/lps_ec/GL3.frg | 51 + src/data/amber_q/lps_ec/GN1.frg | 55 + src/data/amber_q/lps_ec/GN2.frg | 53 + src/data/amber_q/lps_ec/HE1.frg | 55 + src/data/amber_q/lps_ec/HE2.frg | 51 + src/data/amber_q/lps_ec/HE3.frg | 63 + src/data/amber_q/lps_ec/HE4.frg | 63 + src/data/amber_q/lps_ec/KD1.frg | 57 + src/data/amber_q/lps_ec/KD2.frg | 65 + src/data/amber_q/lps_ec/PO4.frg | 18 + src/data/amber_q/lps_ec/POC.frg | 35 + src/data/amber_q/lps_ec/POH.frg | 28 + src/data/amber_q/lps_ec/PT1.frg | 40 + src/data/amber_q/lps_ec/PT2.frg | 38 + src/data/amber_s/ACE.frg | 14 + src/data/amber_s/ACE_N.sgm | 47 + src/data/amber_s/ALA.frg | 16 + src/data/amber_s/ALA.sgm | 102 + src/data/amber_s/ALA_C.frg | 24 + src/data/amber_s/ALA_C.sgm | 117 + src/data/amber_s/ALA_N.frg | 26 + src/data/amber_s/ALA_N.sgm | 131 + src/data/amber_s/ARG.frg | 50 + src/data/amber_s/ARG.sgm | 291 ++ src/data/amber_s/ARG_C.frg | 38 + src/data/amber_s/ARG_C.sgm | 301 ++ src/data/amber_s/ARG_N.frg | 54 + src/data/amber_s/ARG_N.sgm | 315 ++ src/data/amber_s/ASH.frg | 28 + src/data/amber_s/ASH.sgm | 139 + src/data/amber_s/ASN.frg | 30 + src/data/amber_s/ASN.sgm | 157 + src/data/amber_s/ASN_C.frg | 24 + src/data/amber_s/ASN_C.sgm | 169 + src/data/amber_s/ASN_N.frg | 34 + src/data/amber_s/ASN_N.sgm | 183 ++ src/data/amber_s/ASP.frg | 26 + src/data/amber_s/ASP.sgm | 130 + src/data/amber_s/ASP_C.frg | 28 + src/data/amber_s/ASP_C.sgm | 145 + src/data/amber_s/ASP_N.frg | 30 + src/data/amber_s/ASP_N.sgm | 159 + src/data/amber_s/CYM.frg | 22 + src/data/amber_s/CYS.frg | 24 + src/data/amber_s/CYS.sgm | 115 + src/data/amber_s/CYS_C.frg | 19 + src/data/amber_s/CYS_C.sgm | 129 + src/data/amber_s/CYS_N.frg | 28 + src/data/amber_s/CYS_N.sgm | 143 + src/data/amber_s/CYX.frg | 22 + src/data/amber_s/CYX.sgm | 101 + src/data/amber_s/CYX1.sgm | 107 + src/data/amber_s/CYX2.sgm | 101 + src/data/amber_s/CYX_C.frg | 24 + src/data/amber_s/CYX_C.sgm | 117 + src/data/amber_s/CYX_N.frg | 26 + src/data/amber_s/Cl.frg | 8 + src/data/amber_s/Cl.sgm | 7 + src/data/amber_s/DA.frg | 70 + src/data/amber_s/DA_3.frg | 72 + src/data/amber_s/DA_5.frg | 66 + src/data/amber_s/DA_M.frg | 68 + src/data/amber_s/DC.frg | 65 + src/data/amber_s/DC_3.frg | 67 + src/data/amber_s/DC_5.frg | 61 + src/data/amber_s/DC_M.frg | 63 + src/data/amber_s/DG.frg | 72 + src/data/amber_s/DG_3.frg | 74 + src/data/amber_s/DG_5.frg | 68 + src/data/amber_s/DG_M.frg | 70 + src/data/amber_s/DT.frg | 69 + src/data/amber_s/DT_3.frg | 71 + src/data/amber_s/DT_5.frg | 65 + src/data/amber_s/DT_M.frg | 67 + src/data/amber_s/FE.frg | 8 + src/data/amber_s/GLH.frg | 34 + src/data/amber_s/GLH.sgm | 181 ++ src/data/amber_s/GLN.frg | 36 + src/data/amber_s/GLN.sgm | 195 ++ src/data/amber_s/GLN_C.frg | 38 + src/data/amber_s/GLN_C.sgm | 211 ++ src/data/amber_s/GLN_N.frg | 40 + src/data/amber_s/GLN_N.sgm | 225 ++ src/data/amber_s/GLU.frg | 32 + src/data/amber_s/GLU.sgm | 175 + src/data/amber_s/GLU_C.frg | 34 + src/data/amber_s/GLU_C.sgm | 187 ++ src/data/amber_s/GLU_N.frg | 36 + src/data/amber_s/GLU_N.sgm | 201 ++ src/data/amber_s/GLY.frg | 12 + src/data/amber_s/GLY.sgm | 59 + src/data/amber_s/GLY_C.frg | 18 + src/data/amber_s/GLY_C.sgm | 75 + src/data/amber_s/GLY_N.frg | 20 + src/data/amber_s/GLY_N.sgm | 89 + src/data/amber_s/HID.frg | 26 + src/data/amber_s/HID.sgm | 215 ++ src/data/amber_s/HID_C.frg | 28 + src/data/amber_s/HID_C.sgm | 225 ++ src/data/amber_s/HID_N.frg | 29 + src/data/amber_s/HID_N.sgm | 239 ++ src/data/amber_s/HIE.frg | 26 + src/data/amber_s/HIE.sgm | 215 ++ src/data/amber_s/HIE_C.frg | 28 + src/data/amber_s/HIE_C.sgm | 225 ++ src/data/amber_s/HIE_N.frg | 29 + src/data/amber_s/HIE_N.sgm | 239 ++ src/data/amber_s/HIP.frg | 28 + src/data/amber_s/HIP.sgm | 232 ++ src/data/amber_s/HIP_C.frg | 30 + src/data/amber_s/HIP_C.sgm | 243 ++ src/data/amber_s/HIP_N.frg | 31 + src/data/amber_s/HIP_N.sgm | 257 ++ src/data/amber_s/HOH.frg | 8 + src/data/amber_s/ILE.frg | 40 + src/data/amber_s/ILE.sgm | 231 ++ src/data/amber_s/ILE_C.frg | 31 + src/data/amber_s/ILE_C.sgm | 243 ++ src/data/amber_s/ILE_N.frg | 44 + src/data/amber_s/ILE_N.sgm | 257 ++ src/data/amber_s/IM.frg | 4 + src/data/amber_s/IM.sgm | 7 + src/data/amber_s/IP.frg | 4 + src/data/amber_s/K.frg | 8 + src/data/amber_s/K.sgm | 7 + src/data/amber_s/LEU.frg | 40 + src/data/amber_s/LEU.sgm | 231 ++ src/data/amber_s/LEU_C.frg | 42 + src/data/amber_s/LEU_C.sgm | 243 ++ src/data/amber_s/LEU_N.frg | 44 + src/data/amber_s/LEU_N.sgm | 257 ++ src/data/amber_s/LYN.frg | 44 + src/data/amber_s/LYS.frg | 46 + src/data/amber_s/LYS.sgm | 269 ++ src/data/amber_s/LYS_C.frg | 34 + src/data/amber_s/LYS_C.sgm | 285 ++ 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src/data/charmm_s/GLU_C.frg create mode 100644 src/data/charmm_s/GLU_N.frg create mode 100644 src/data/charmm_s/GLY.frg create mode 100644 src/data/charmm_s/GLY_C.frg create mode 100644 src/data/charmm_s/GLY_N.frg create mode 100644 src/data/charmm_s/HEME.frg create mode 100644 src/data/charmm_s/HSD.frg create mode 100644 src/data/charmm_s/HSD_C.frg create mode 100644 src/data/charmm_s/HSD_N.frg create mode 100644 src/data/charmm_s/HSE.frg create mode 100644 src/data/charmm_s/HSE_C.frg create mode 100644 src/data/charmm_s/HSE_N.frg create mode 100644 src/data/charmm_s/HSP.frg create mode 100644 src/data/charmm_s/HSP_C.frg create mode 100644 src/data/charmm_s/HSP_N.frg create mode 100644 src/data/charmm_s/ILE.frg create mode 100644 src/data/charmm_s/ILE_C.frg create mode 100644 src/data/charmm_s/ILE_N.frg create mode 100644 src/data/charmm_s/LEU.frg create mode 100644 src/data/charmm_s/LEU_C.frg create mode 100644 src/data/charmm_s/LEU_N.frg create mode 100644 src/data/charmm_s/LYS.frg create mode 100644 src/data/charmm_s/LYS_C.frg create mode 100644 src/data/charmm_s/LYS_N.frg create mode 100644 src/data/charmm_s/MET.frg create mode 100644 src/data/charmm_s/MET_C.frg create mode 100644 src/data/charmm_s/MET_N.frg create mode 100644 src/data/charmm_s/O2.frg create mode 100644 src/data/charmm_s/PHE.frg create mode 100644 src/data/charmm_s/PHE_C.frg create mode 100644 src/data/charmm_s/PHE_N.frg create mode 100644 src/data/charmm_s/PRO.frg create mode 100644 src/data/charmm_s/PRO_C.frg create mode 100644 src/data/charmm_s/PRO_N.frg create mode 100644 src/data/charmm_s/SER.frg create mode 100644 src/data/charmm_s/SER_C.frg create mode 100644 src/data/charmm_s/SER_N.frg create mode 100644 src/data/charmm_s/THR.frg create mode 100644 src/data/charmm_s/THR_C.frg create mode 100644 src/data/charmm_s/THR_N.frg create mode 100644 src/data/charmm_s/TIP3.frg create mode 100644 src/data/charmm_s/TP3M.frg create mode 100644 src/data/charmm_s/TRP.frg create mode 100644 src/data/charmm_s/TRP_C.frg create mode 100644 src/data/charmm_s/TRP_N.frg create mode 100644 src/data/charmm_s/TYR.frg create mode 100644 src/data/charmm_s/TYR_C.frg create mode 100644 src/data/charmm_s/TYR_N.frg create mode 100644 src/data/charmm_s/VAL.frg create mode 100644 src/data/charmm_s/VAL_C.frg create mode 100644 src/data/charmm_s/VAL_N.frg create mode 100644 src/data/charmm_s/ZN2.frg create mode 100644 src/data/charmm_s/charmm.par create mode 100644 src/data/charmm_s/par_all27_na_lipid.par create mode 100644 src/data/charmm_s/par_all27_prot_lipid.par create mode 100644 src/data/charmm_s/par_all27_prot_na.par create mode 100644 src/data/charmm_s/par_all32_lipid.par create mode 100644 src/data/charmm_s/par_all35_ethers.par create mode 100644 src/data/charmm_x/GLU_C.frg create mode 100644 src/data/charmm_x/MET_N.frg create mode 100644 src/data/charmm_x/Na.frg create mode 100644 src/data/charmm_x/Na_M.frg create mode 100644 src/data/charmm_x/spce.sgm create mode 100644 src/data/charmm_x/spce_M.sgm create mode 100644 src/data/solvents/clfm.rst create mode 100644 src/data/solvents/meoh.rst create mode 100644 src/data/solvents/spce.rst create mode 100644 src/data/solvents/thfs.rst diff --git a/src/data/amber_q/ABE.frg b/src/data/amber_q/ABE.frg new file mode 100644 index 0000000..1db6ccd --- /dev/null +++ b/src/data/amber_q/ABE.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$ABE + 20 1 1 0 +ABE + 1 C1 AC 3 0 0 1 1 -0.252626 0.000000 + 2 H1 H2 0 0 0 1 1 0.216755 0.000000 + 3 C2 CT 0 0 0 1 1 0.277475 0.000000 + 4 H2 H1 0 0 0 1 1 0.092812 0.000000 + 5 O2 OH 0 0 0 1 1 -0.608823 0.000000 + 6 HO2 HO 0 0 0 1 1 0.364969 0.000000 + 7 C3 CT 0 0 0 1 1 -0.146592 0.000000 + 82H3 HC 0 0 0 1 1 0.073592 0.000000 + 93H3 HC 0 0 0 1 1 0.073592 0.000000 + 10 C4 CT 0 0 0 1 1 0.153661 0.000000 + 11 H4 H1 0 0 0 1 1 0.042781 0.000000 + 12 O4 OH 0 0 0 1 1 -0.550610 0.000000 + 13 HO4 HO 0 0 0 1 1 0.362947 0.000000 + 14 C5 CT 0 0 0 1 1 0.114707 0.000000 + 15 H5 H1 0 0 0 1 1 0.062819 0.000000 + 16 OR OS 0 0 0 1 1 -0.276948 0.000000 + 17 C6 CT 0 0 0 1 1 -0.225880 0.000000 + 182H6 HC 0 0 0 1 1 0.075123 0.000000 + 193H6 HC 0 0 0 1 1 0.075123 0.000000 + 204H6 HC 0 0 0 1 1 0.075123 0.000000 + 1 2 + 1 3 + 1 16 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/BNZ.frg b/src/data/amber_q/BNZ.frg new file mode 100644 index 0000000..39d8b1b --- /dev/null +++ b/src/data/amber_q/BNZ.frg @@ -0,0 +1,23 @@ +# Fragment definition for benzene +$benzene + 12 1 1 0 +benzen + 1 C1 CA 0 0 0 1 1 -0.060000 0.000000 + 2 H1 HA 0 0 0 1 1 0.060000 0.000000 + 3 C2 CA 0 0 0 1 1 -0.060000 0.000000 + 4 H2 HA 0 0 0 1 1 0.060000 0.000000 + 5 C3 CA 0 0 0 1 1 -0.060000 0.000000 + 6 H3 HA 0 0 0 1 1 0.060000 0.000000 + 7 C4 CA 0 0 0 1 1 -0.060000 0.000000 + 8 H4 HA 0 0 0 1 1 0.060000 0.000000 + 9 C5 CA 0 0 0 1 1 -0.060000 0.000000 + 10 H5 HA 0 0 0 1 1 0.060000 0.000000 + 11 C6 CA 0 0 0 1 1 -0.060000 0.000000 + 12 H6 HA 0 0 0 1 1 0.060000 0.000000 + 1 3 5 7 9 11 1 + 1 2 + 3 4 + 5 6 + 7 8 + 9 10 + 11 12 diff --git a/src/data/amber_q/BTH.frg b/src/data/amber_q/BTH.frg new file mode 100644 index 0000000..be37cbc --- /dev/null +++ b/src/data/amber_q/BTH.frg @@ -0,0 +1,28 @@ +# This is an automatically generated fragment file +# +$BTH + 12 1 1 0 +BTH + 1 C1 CT 3 0 0 1 1 -0.021034 0.000000 + 22H1 HC 0 0 0 1 1 0.010517 0.000000 + 33H1 HC 0 0 0 1 1 0.010517 0.000000 + 4 C2 CT 0 0 0 1 1 -0.012697 0.000000 + 52H2 HC 0 0 0 1 1 0.006349 0.000000 + 63H2 HC 0 0 0 1 1 0.006349 0.000000 + 7 C3 CT 0 0 0 1 1 -0.024254 0.000000 + 82H3 HC 0 0 0 1 1 0.012127 0.000000 + 93H3 HC 0 0 0 1 1 0.012127 0.000000 + 10 C4 CT 4 0 0 1 1 -0.010029 0.000000 + 112H4 HC 0 0 0 1 1 0.005014 0.000000 + 123H4 HC 0 0 0 1 1 0.005014 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 diff --git a/src/data/amber_q/BTH.sgm b/src/data/amber_q/BTH.sgm new file mode 100644 index 0000000..895e2d9 --- /dev/null +++ b/src/data/amber_q/BTH.sgm @@ -0,0 +1,129 @@ +# This is an automatically generated segment file +# + 4.600000 + 12 11 18 21 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.100000 0.000000 + 22H1 0 0 0 1 1 + HC 0.050000 0.000000 + 33H1 0 0 0 1 1 + HC 0.050000 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 4 0 0 1 1 + CT -0.100000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 4 5 0 0 + 0.000000 0.00000E+00 + 5 1 4 6 0 0 + 0.000000 0.00000E+00 + 6 1 4 7 0 0 + 0.000000 0.00000E+00 + 7 5 4 6 0 0 + 0.000000 0.00000E+00 + 8 5 4 7 0 0 + 0.000000 0.00000E+00 + 9 6 4 7 0 0 + 0.000000 0.00000E+00 + 10 4 7 8 0 0 + 0.000000 0.00000E+00 + 11 4 7 9 0 0 + 0.000000 0.00000E+00 + 12 4 7 10 0 0 + 0.000000 0.00000E+00 + 13 8 7 9 0 0 + 0.000000 0.00000E+00 + 14 8 7 10 0 0 + 0.000000 0.00000E+00 + 15 9 7 10 0 0 + 0.000000 0.00000E+00 + 16 7 10 11 0 0 + 0.000000 0.00000E+00 + 17 7 10 12 0 0 + 0.000000 0.00000E+00 + 18 11 10 12 0 0 + 0.000000 0.00000E+00 + 1 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 8 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 9 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 10 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 17 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 18 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 19 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 20 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 21 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/BTO.frg b/src/data/amber_q/BTO.frg new file mode 100644 index 0000000..5e0d4fe --- /dev/null +++ b/src/data/amber_q/BTO.frg @@ -0,0 +1,26 @@ +# This is an automatically generated fragment file +# +$BTO + 11 1 1 0 +BTO + 1 C1 C 3 1 0 1 1 0.190650 0.000000 + 2 O1 O2 0 0 0 1 1 -0.340348 0.000000 + 3 C2 CT 0 0 0 1 1 -0.043202 0.000000 + 42H2 HC 0 0 0 1 1 0.059487 0.000000 + 53H2 HC 0 0 0 1 1 0.059487 0.000000 + 6 C3 CT 0 0 0 1 1 0.014628 0.000000 + 72H3 HC 0 0 0 1 1 0.039814 0.000000 + 83H3 HC 0 0 0 1 1 0.039814 0.000000 + 9 C4 CT 4 0 0 1 1 -0.003054 0.000000 + 102H4 HC 0 0 0 1 1 -0.008638 0.000000 + 113H4 HC 0 0 0 1 1 -0.008638 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 diff --git a/src/data/amber_q/BTO.sgm b/src/data/amber_q/BTO.sgm new file mode 100644 index 0000000..f404384 --- /dev/null +++ b/src/data/amber_q/BTO.sgm @@ -0,0 +1,115 @@ +# This is an automatically generated segment file +# + 4.600000 + 11 10 16 18 0 0 1 1 + 0.000000 + 1 C1 3 1 0 1 1 + C 0.325525 0.000000 + 2 O1 0 0 0 1 1 + O2 -0.406899 0.000000 + 3 C2 0 0 0 1 1 + CT -0.111850 0.000000 + 42H2 0 0 0 1 1 + HC 0.096612 0.000000 + 53H2 0 0 0 1 1 + HC 0.096612 0.000000 + 6 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 72H3 0 0 0 1 1 + HC 0.050000 0.000000 + 83H3 0 0 0 1 1 + HC 0.050000 0.000000 + 9 C4 4 0 0 1 1 + CT -0.100000 0.000000 + 102H4 0 0 0 1 1 + HC 0.050000 0.000000 + 113H4 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 6 0 0 + 0.000000 0.00000E+00 + 6 6 7 0 0 + 0.000000 0.00000E+00 + 7 6 8 0 0 + 0.000000 0.00000E+00 + 8 6 9 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 10 9 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 6 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 6 0 0 + 0.000000 0.00000E+00 + 7 5 3 6 0 0 + 0.000000 0.00000E+00 + 8 3 6 7 0 0 + 0.000000 0.00000E+00 + 9 3 6 8 0 0 + 0.000000 0.00000E+00 + 10 3 6 9 0 0 + 0.000000 0.00000E+00 + 11 7 6 8 0 0 + 0.000000 0.00000E+00 + 12 7 6 9 0 0 + 0.000000 0.00000E+00 + 13 8 6 9 0 0 + 0.000000 0.00000E+00 + 14 6 9 10 0 0 + 0.000000 0.00000E+00 + 15 6 9 11 0 0 + 0.000000 0.00000E+00 + 16 10 9 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 6 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 6 7 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 6 8 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 6 9 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 6 7 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 6 8 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 6 9 0 0 + 0 0.000000 0.00000E+00 + 10 5 3 6 7 0 0 + 0 0.000000 0.00000E+00 + 11 5 3 6 8 0 0 + 0 0.000000 0.00000E+00 + 12 5 3 6 9 0 0 + 0 0.000000 0.00000E+00 + 13 3 6 9 10 0 0 + 0 0.000000 0.00000E+00 + 14 3 6 9 11 0 0 + 0 0.000000 0.00000E+00 + 15 7 6 9 10 0 0 + 0 0.000000 0.00000E+00 + 16 7 6 9 11 0 0 + 0 0.000000 0.00000E+00 + 17 8 6 9 10 0 0 + 0 0.000000 0.00000E+00 + 18 8 6 9 11 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/BUT.frg b/src/data/amber_q/BUT.frg new file mode 100644 index 0000000..e763e5f --- /dev/null +++ b/src/data/amber_q/BUT.frg @@ -0,0 +1,30 @@ +# This is an automatically generated fragment file +# +$BUT + 13 1 1 0 +BUT + 1 C1 CT 3 0 0 1 1 -0.011176 0.000000 + 22H1 HC 0 0 0 1 1 0.005588 0.000000 + 33H1 HC 0 0 0 1 1 0.005588 0.000000 + 4 C2 CT 0 0 0 1 1 -0.023686 0.000000 + 52H2 HC 0 0 0 1 1 0.011843 0.000000 + 63H2 HC 0 0 0 1 1 0.011843 0.000000 + 7 C3 CT 0 0 0 1 1 -0.006136 0.000000 + 82H3 HC 0 0 0 1 1 0.003068 0.000000 + 93H3 HC 0 0 0 1 1 0.003068 0.000000 + 10 C4 CT 0 0 0 1 1 0.091023 0.000000 + 112H4 HC 0 0 0 1 1 -0.030341 0.000000 + 123H4 HC 0 0 0 1 1 -0.030341 0.000000 + 134H4 HC 0 0 0 1 1 -0.030341 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 diff --git a/src/data/amber_q/BUT.sgm b/src/data/amber_q/BUT.sgm new file mode 100644 index 0000000..61066e1 --- /dev/null +++ b/src/data/amber_q/BUT.sgm @@ -0,0 +1,145 @@ +# This is an automatically generated segment file +# + 4.600000 + 13 12 21 24 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.100000 0.000000 + 22H1 0 0 0 1 1 + HC 0.050000 0.000000 + 33H1 0 0 0 1 1 + HC 0.050000 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 0 0 0 1 1 + CT -0.150000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 134H4 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 12 10 13 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 4 5 0 0 + 0.000000 0.00000E+00 + 5 1 4 6 0 0 + 0.000000 0.00000E+00 + 6 1 4 7 0 0 + 0.000000 0.00000E+00 + 7 5 4 6 0 0 + 0.000000 0.00000E+00 + 8 5 4 7 0 0 + 0.000000 0.00000E+00 + 9 6 4 7 0 0 + 0.000000 0.00000E+00 + 10 4 7 8 0 0 + 0.000000 0.00000E+00 + 11 4 7 9 0 0 + 0.000000 0.00000E+00 + 12 4 7 10 0 0 + 0.000000 0.00000E+00 + 13 8 7 9 0 0 + 0.000000 0.00000E+00 + 14 8 7 10 0 0 + 0.000000 0.00000E+00 + 15 9 7 10 0 0 + 0.000000 0.00000E+00 + 16 7 10 11 0 0 + 0.000000 0.00000E+00 + 17 7 10 12 0 0 + 0.000000 0.00000E+00 + 18 7 10 13 0 0 + 0.000000 0.00000E+00 + 19 11 10 12 0 0 + 0.000000 0.00000E+00 + 20 11 10 13 0 0 + 0.000000 0.00000E+00 + 21 12 10 13 0 0 + 0.000000 0.00000E+00 + 1 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 8 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 9 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 10 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 17 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 18 4 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 19 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 20 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 21 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 22 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 24 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/CA.frg b/src/data/amber_q/CA.frg new file mode 100644 index 0000000..6dd05de --- /dev/null +++ b/src/data/amber_q/CA.frg @@ -0,0 +1,5 @@ +# Fragment definition for Calcium cation +$CA + 1 1 1 0 +CA + 1CA Ca 0 0 0 1 1 2.000000 0.000000 diff --git a/src/data/amber_q/CTR.frg b/src/data/amber_q/CTR.frg new file mode 100644 index 0000000..4c94153 --- /dev/null +++ b/src/data/amber_q/CTR.frg @@ -0,0 +1,13 @@ +# C-terminal cap fragment +# +$CTR + 6 1 1 0 +CTR + 1 C1 CT 0 0 0 1 1 -0.150000 0.000000 + 22H1 H1 0 0 0 1 1 0.050000 0.000000 + 33H1 H1 0 0 0 1 1 0.050000 0.000000 + 44H1 H1 0 0 0 1 1 0.050000 0.000000 + 5 N N 3 0 0 1 1 -0.415700 0.000000 + 6 H H 0 0 0 1 1 0.415700 0.000000 + 2 1 5 6 + 3 1 4 diff --git a/src/data/amber_q/Ca.sgm b/src/data/amber_q/Ca.sgm new file mode 100644 index 0000000..3d15ec2 --- /dev/null +++ b/src/data/amber_q/Ca.sgm @@ -0,0 +1,7 @@ +# This is an automatically generated segment file +# + 4.600000 + 1 0 0 0 0 0 1 1 + 0.000000 + 1Ca 0 0 0 1 1 + Ca 2.000000 0.000000 diff --git a/src/data/amber_q/DTT.frg b/src/data/amber_q/DTT.frg new file mode 100644 index 0000000..7c03306 --- /dev/null +++ b/src/data/amber_q/DTT.frg @@ -0,0 +1,92 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$DTT + 42 1 1 0 +DTT + 1 N1 N* 0 6 0 1 1 -0.023900 0.000000 + 2 C2 C 0 6 0 1 1 0.567700 0.000000 + 3 N3 NA 0 6 0 1 1 -0.434000 0.000000 + 4 H3 H 0 0 0 1 1 0.342000 0.000000 + 5 C4 C 0 6 0 1 1 0.519400 0.000000 + 6 C5 CM 0 6 0 1 1 0.002500 0.000000 + 7 C5M CT 0 0 0 1 1 -0.226900 0.000000 + 82H5M HC 0 0 0 1 1 0.077000 0.000000 + 93H5M HC 0 0 0 1 1 0.077000 0.000000 + 104H5M HC 0 0 0 1 1 0.077000 0.000000 + 11 C6 CM 0 6 0 1 1 -0.220900 0.000000 + 122H6 H4 0 0 0 1 1 0.260700 0.000000 + 13 O2 O 0 0 0 1 1 -0.588100 0.000000 + 14 O4 O 0 0 0 1 1 -0.556300 0.000000 + 15 C1* CT 0 0 0 1 1 0.068000 0.000000 + 162H1* H2 0 0 0 1 1 0.180400 0.000000 + 17 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 182H2* HC 0 0 0 1 1 0.071800 0.000000 + 193H2* HC 0 0 0 1 1 0.071800 0.000000 + 20 C3* CT 0 0 0 1 1 0.071300 0.000000 + 212H3* H1 0 0 0 1 1 0.098500 0.000000 + 22 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 233H3* HO 0 0 0 1 1 0.439600 0.000000 + 24 C4* CT 0 0 0 1 1 0.162900 0.000000 + 252H4* H1 0 0 0 1 1 0.117600 0.000000 + 26 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 27 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 282H5* H1 0 0 0 1 1 0.075400 0.000000 + 293H5* H1 0 0 0 1 1 0.075400 0.000000 + 30 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 31 PA P 0 0 0 1 1 1.145727 0.000000 + 32 O1A O2 0 0 0 1 1 -0.721001 0.000000 + 33 O2A O2 0 0 0 1 1 -0.721001 0.000000 + 34 O3A OS 0 0 0 1 1 -0.390741 0.000000 + 35 PB P 0 0 0 1 1 1.240313 0.000000 + 36 O1B O2 0 0 0 1 1 -0.765956 0.000000 + 37 O2B O2 0 0 0 1 1 -0.765956 0.000000 + 38 O3B OS 0 0 0 1 1 -0.769623 0.000000 + 39 PG P 0 0 0 1 1 1.164170 0.000000 + 40 O1G O2 0 0 0 1 1 -0.907458 0.000000 + 41 O2G O2 0 0 0 1 1 -0.907458 0.000000 + 42 O3G O2 0 0 0 1 1 -0.907458 0.000000 + 1 2 + 1 11 + 1 15 + 2 3 + 2 13 + 3 4 + 3 5 + 5 6 + 5 14 + 6 7 + 6 11 + 7 8 + 7 9 + 7 10 + 11 12 + 15 16 + 15 17 + 15 26 + 17 18 + 17 19 + 17 20 + 20 21 + 20 22 + 20 24 + 22 23 + 24 25 + 24 26 + 24 27 + 27 28 + 27 29 + 27 30 + 30 31 + 31 32 + 31 33 + 31 34 + 34 35 + 35 36 + 35 37 + 35 38 + 38 39 + 39 40 + 39 41 + 39 42 diff --git a/src/data/amber_q/EAM.frg b/src/data/amber_q/EAM.frg new file mode 100644 index 0000000..e56f6ee --- /dev/null +++ b/src/data/amber_q/EAM.frg @@ -0,0 +1,24 @@ +# This is an automatically generated fragment file +# +$EAM + 10 1 1 0 +EAM + 1 C1 CT 3 0 0 1 1 -0.064862 0.000000 + 22H1 H1 0 0 0 1 1 0.086747 0.000000 + 33H1 H1 0 0 0 1 1 0.086747 0.000000 + 4 C2 CT 0 0 0 1 1 0.188179 0.000000 + 52H2 HP 0 0 0 1 1 0.044255 0.000000 + 63H2 HP 0 0 0 1 1 0.044255 0.000000 + 7 N3 N3 0 0 0 1 1 -0.202182 0.000000 + 82H3 H 0 0 0 1 1 0.272287 0.000000 + 93H3 H 0 0 0 1 1 0.272287 0.000000 + 104H3 H 0 0 0 1 1 0.272287 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 diff --git a/src/data/amber_q/FUC.sgm b/src/data/amber_q/FUC.sgm new file mode 100644 index 0000000..eb416f1 --- /dev/null +++ b/src/data/amber_q/FUC.sgm @@ -0,0 +1,339 @@ +# This is an automatically generated segment file +# + 4.600000 + 26 26 47 66 2 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + EC -0.369000 40.000000 + 2 H1 0 0 0 1 1 + H2 0.220660 40.000000 + 3 OR 0 0 0 1 1 + OS 0.030570 90.000000 + 4 C2 0 0 0 1 1 + CT 0.015000 0.000000 + 5 H2 0 0 0 1 1 + H1 0.193480 60.000000 + 6 N1 0 1 0 1 1 + N -0.327260 70.000000 + 7 HN1 0 0 0 1 1 + H 0.281180 0.000000 + 8 C21 0 1 0 1 1 + C 0.522110 60.000000 + 9 O21 0 0 0 1 1 + O -0.618400 50.000000 + 10 C22 0 0 0 1 1 + CT -0.185560 0.000000 + 112H22 0 0 0 1 1 + HC 0.061850 30.000000 + 123H22 0 0 0 1 1 + HC 0.061850 30.000000 + 134H22 0 0 0 1 1 + HC 0.061850 30.000000 + 14 C3 0 0 0 1 1 + CT -0.064040 70.000000 + 15 H3 0 0 0 1 1 + H1 0.197770 10.000000 + 16 O3 4 0 0 1 1 + OS -0.139340 60.000000 + 17 C4 0 0 0 1 1 + CT 0.089130 80.000000 + 18 H4 0 0 0 1 1 + H1 0.087350 80.000000 + 19 O4 0 0 0 1 1 + OH -0.574490 90.000000 + 20 HO4 0 0 0 1 1 + HO 0.371410 50.000000 + 21 C5 0 0 0 1 1 + CT 0.055220 20.000000 + 22 H5 0 0 0 1 1 + H1 0.028670 0.000000 + 23 C6 0 0 0 1 1 + CT -0.184120 10.000000 + 242H6 0 0 0 1 1 + HC 0.061370 40.000000 + 253H6 0 0 0 1 1 + HC 0.061370 40.000000 + 264H6 0 0 0 1 1 + HC 0.061370 40.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 21 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 14 0 0 + 0.000000 0.00000E+00 + 8 6 7 0 0 + 0.000000 0.00000E+00 + 9 6 8 0 0 + 0.000000 0.00000E+00 + 10 8 9 0 0 + 0.000000 0.00000E+00 + 11 8 10 0 0 + 0.000000 0.00000E+00 + 12 10 11 0 0 + 0.000000 0.00000E+00 + 13 10 12 0 0 + 0.000000 0.00000E+00 + 14 10 13 0 0 + 0.000000 0.00000E+00 + 15 14 15 0 0 + 0.000000 0.00000E+00 + 16 14 16 0 0 + 0.000000 0.00000E+00 + 17 14 17 0 0 + 0.000000 0.00000E+00 + 18 17 18 0 0 + 0.000000 0.00000E+00 + 19 17 19 0 0 + 0.000000 0.00000E+00 + 20 17 21 0 0 + 0.000000 0.00000E+00 + 21 19 20 0 0 + 0.000000 0.00000E+00 + 22 21 22 0 0 + 0.000000 0.00000E+00 + 23 21 23 0 0 + 0.000000 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0.00000E+00 diff --git a/src/data/amber_q/G31.frg b/src/data/amber_q/G31.frg new file mode 100644 index 0000000..3b28f5f --- /dev/null +++ b/src/data/amber_q/G31.frg @@ -0,0 +1,33 @@ +# This is an automatically generated fragment file +# +$G31 + 21 1 1 0 +G31 + 1 C1 AC 3 0 0 1 1 0.056660 0.000000 + 2 H1 H2 0 0 0 1 1 0.116313 0.000000 + 3 C2 CT 0 0 0 1 1 0.348685 0.000000 + 4 H2 H1 0 0 0 1 1 -0.005043 0.000000 + 5 O2 OH 0 0 0 1 1 -0.534391 0.000000 + 6 HO2 HO 0 0 0 1 1 0.282172 0.000000 + 7 C3 CT 0 0 0 1 1 0.491508 0.000000 + 8 H3 H1 0 0 0 1 1 -0.052923 0.000000 + 9 O3 OG 4 0 0 1 1 -0.362832 0.000000 + 10 C4 CT 0 0 0 1 1 -0.002668 0.000000 + 11 H4 H1 0 0 0 1 1 0.072986 0.000000 + 12 O4 OH 0 0 0 1 1 -0.694477 0.000000 + 13 HO4 HO 0 0 0 1 1 0.364249 0.000000 + 14 C5 CT 0 0 0 1 1 0.359572 0.000000 + 15 H5 H1 0 0 0 1 1 -0.059894 0.000000 + 16 OR OS 0 0 0 1 1 -0.469228 0.000000 + 17 C6 CT 0 0 0 1 1 0.410261 0.000000 + 182H6 H1 0 0 0 1 1 -0.002202 0.000000 + 193H6 H1 0 0 0 1 1 -0.002202 0.000000 + 20 O6 OH 0 0 0 1 1 -0.759579 0.000000 + 21 HO6 HO 0 0 0 1 1 0.443033 0.000000 + 1 3 7 10 14 16 1 + 2 1 + 4 3 5 6 + 8 7 9 + 11 10 12 13 + 15 14 17 20 21 + 18 17 19 diff --git a/src/data/amber_q/G61.frg b/src/data/amber_q/G61.frg new file mode 100644 index 0000000..cbaa48b --- /dev/null +++ b/src/data/amber_q/G61.frg @@ -0,0 +1,33 @@ +# This is an automatically generated fragment file +# +$G61 + 21 1 1 0 +G61 + 1 C1 AC 3 0 0 1 1 -0.082413 0.000000 + 2 H1 H2 0 0 0 1 1 0.149744 0.000000 + 3 C2 CT 0 0 0 1 1 0.518148 0.000000 + 4 H2 H1 0 0 0 1 1 -0.024679 0.000000 + 5 O2 OH 0 0 0 1 1 -0.727593 0.000000 + 6 HO2 HO 0 0 0 1 1 0.377372 0.000000 + 7 C3 CT 0 0 0 1 1 0.449012 0.000000 + 8 H3 H1 0 0 0 1 1 -0.115875 0.000000 + 9 O3 OH 0 0 0 1 1 -0.756429 0.000000 + 10 HO3 HO 0 0 0 1 1 0.432471 0.000000 + 11 C4 CT 0 0 0 1 1 0.483802 0.000000 + 12 H4 H1 0 0 0 1 1 -0.046401 0.000000 + 13 O4 OH 0 0 0 1 1 -0.846824 0.000000 + 14 HO4 HO 0 0 0 1 1 0.480784 0.000000 + 15 C5 CT 0 0 0 1 1 -0.030941 0.000000 + 16 H5 H1 0 0 0 1 1 -0.003503 0.000000 + 17 OR OS 0 0 0 1 1 -0.331900 0.000000 + 18 C6 CT 0 0 0 1 1 0.255276 0.000000 + 192H6 H1 0 0 0 1 1 0.017280 0.000000 + 203H6 H1 0 0 0 1 1 0.017280 0.000000 + 21 O6 OG 4 0 0 1 1 -0.214611 0.000000 + 1 3 7 11 15 17 1 + 2 1 + 4 3 5 6 + 8 7 9 10 + 12 11 13 14 + 16 15 18 21 + 19 18 20 diff --git a/src/data/amber_q/G64.frg b/src/data/amber_q/G64.frg new file mode 100644 index 0000000..34c1ff3 --- /dev/null +++ b/src/data/amber_q/G64.frg @@ -0,0 +1,32 @@ +# This is an automatically generated fragment file +# +$G64 + 20 1 1 0 +G64 + 1 C1 AC 3 0 0 1 1 0.175807 0.000000 + 2 H1 H2 0 0 0 1 1 0.073262 0.000000 + 3 C2 CT 0 0 0 1 1 0.591933 0.000000 + 4 H2 H1 0 0 0 1 1 -0.066911 0.000000 + 5 O2 OH 0 0 0 1 1 -0.640479 0.000000 + 6 HO2 HO 0 0 0 1 1 0.279817 0.000000 + 7 C3 CT 0 0 0 1 1 -0.345367 0.000000 + 8 H3 H1 0 0 0 1 1 0.112774 0.000000 + 9 O3 OH 0 0 0 1 1 -0.479863 0.000000 + 10 HO3 HO 0 0 0 1 1 0.294383 0.000000 + 11 C4 CT 0 0 0 1 1 0.481763 0.000000 + 12 H4 H1 0 0 0 1 1 0.130413 0.000000 + 13 O4 OS 4 0 0 1 1 -0.505731 0.000000 + 14 C5 CT 0 0 0 1 1 0.560113 0.000000 + 15 H5 H1 0 0 0 1 1 -0.208270 0.000000 + 16 OR OS 0 0 0 1 1 -0.708454 0.000000 + 17 C6 CT 0 0 0 1 1 0.400858 0.000000 + 182H6 H1 0 0 0 1 1 -0.005751 0.000000 + 193H6 H1 0 0 0 1 1 -0.005751 0.000000 + 20 O6 OG 5 0 0 1 1 -0.134546 0.000000 + 1 3 7 11 14 16 1 + 2 1 + 4 3 5 6 + 8 7 9 10 + 12 11 13 + 15 14 17 20 + 18 17 19 diff --git a/src/data/amber_q/GA1.frg b/src/data/amber_q/GA1.frg new file mode 100644 index 0000000..d814e38 --- /dev/null +++ b/src/data/amber_q/GA1.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# +$GA1 + 22 1 1 0 +GA1 + 1 C1 AC 3 0 0 1 1 -0.067884 0.000000 + 2 H1 H2 0 0 0 1 1 0.151312 0.000000 + 3 OR OS 0 0 0 1 1 -0.319184 0.000000 + 4 C2 CT 0 0 0 1 1 0.147069 0.000000 + 5 H2 H1 0 0 0 1 1 0.164883 0.000000 + 6 O2 OH 0 0 0 1 1 -0.636000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.400609 0.000000 + 8 C3 CT 0 0 0 1 1 0.178265 0.000000 + 9 H3 H1 0 0 0 1 1 0.055354 0.000000 + 10 O3 OH 0 0 0 1 1 -0.637433 0.000000 + 11 HO3 HO 0 0 0 1 1 0.411140 0.000000 + 12 C4 CT 0 0 0 1 1 0.026886 0.000000 + 13 H4 H1 0 0 0 1 1 0.207370 0.000000 + 14 O4 OH 0 0 0 1 1 -0.641959 0.000000 + 15 HO4 HO 0 0 0 1 1 0.420772 0.000000 + 16 C5 CT 0 0 0 1 1 0.068030 0.000000 + 17 H5 H1 0 0 0 1 1 0.095612 0.000000 + 18 C6 CT 0 0 0 1 1 0.062660 0.000000 + 192H6 H1 0 0 0 1 1 0.077289 0.000000 + 203H6 H1 0 0 0 1 1 0.077289 0.000000 + 21 O6 OH 0 0 0 1 1 -0.677054 0.000000 + 22 HO6 HO 0 0 0 1 1 0.434974 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GA2.frg b/src/data/amber_q/GA2.frg new file mode 100644 index 0000000..2b7f4e2 --- /dev/null +++ b/src/data/amber_q/GA2.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# +$GA2 + 21 1 1 0 +GA2 + 1 C1 AC 3 0 0 1 1 0.099978 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0.190000 0.000000 + 19 N N 0 0 0 1 1 -0.410000 0.000000 + 20 HN H 0 0 0 1 1 0.270000 0.000000 + 21 CA CT 0 0 0 1 1 0.020000 0.000000 + 22 HA H1 0 0 0 1 1 0.050000 0.000000 + 23 CB CT 0 0 0 1 1 -0.150000 0.000000 + 242HB HC 0 0 0 1 1 0.050000 0.000000 + 253HB HC 0 0 0 1 1 0.050000 0.000000 + 264HB HC 0 0 0 1 1 0.050000 0.000000 + 27 C C 0 1 0 1 1 0.800000 0.000000 + 28 OC O2 0 0 0 1 1 -0.900000 0.000000 + 29 O O2 0 0 0 1 1 -0.900000 0.000000 + 1 2 + 1 3 + 1 4 + 3 12 + 4 5 + 4 6 + 4 19 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 14 15 + 14 16 + 14 17 + 17 18 + 19 20 + 19 21 + 21 22 + 21 23 + 21 27 + 23 24 + 23 25 + 23 26 + 27 28 + 27 29 diff --git a/src/data/amber_q/GA3.sgm b/src/data/amber_q/GA3.sgm new file mode 100644 index 0000000..7c8b7f7 --- /dev/null +++ b/src/data/amber_q/GA3.sgm @@ -0,0 +1,383 @@ +# This is an automatically generated segment file +# + 4.600000 + 29 29 53 77 1 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC 0.038921 0.000000 + 2 H1 0 0 0 1 1 + H2 0.186521 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-0.181679 0.000000 + 2 H1 H2 0 0 0 1 1 0.235104 0.000000 + 3 C2 CT 0 0 0 1 1 0.036346 0.000000 + 4 H2 H1 0 0 0 1 1 0.149332 0.000000 + 5 O2 OH 0 0 0 1 1 -0.590556 0.000000 + 6 HO2 HO 0 0 0 1 1 0.396247 0.000000 + 7 C3 CT 0 0 0 1 1 0.021948 0.000000 + 8 H3 H1 0 0 0 1 1 0.115040 0.000000 + 9 O3 OG 4 0 0 1 1 -0.113637 0.000000 + 10 C4 CT 0 0 0 1 1 -0.012852 0.000000 + 11 H4 H1 0 0 0 1 1 0.117350 0.000000 + 12 O4 OH 0 0 0 1 1 -0.571279 0.000000 + 13 HO4 HO 0 0 0 1 1 0.390331 0.000000 + 14 C5 CT 0 0 0 1 1 0.073483 0.000000 + 15 H5 H1 0 0 0 1 1 0.115195 0.000000 + 16 OR OS 0 0 0 1 1 -0.218482 0.000000 + 17 C6 CT 0 0 0 1 1 0.043377 0.000000 + 182H6 H1 0 0 0 1 1 0.094261 0.000000 + 193H6 H1 0 0 0 1 1 0.094261 0.000000 + 20 O6 OH 0 0 0 1 1 -0.568221 0.000000 + 21 HO6 HO 0 0 0 1 1 0.374431 0.000000 + 1 2 + 1 3 + 1 16 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 + 20 21 diff --git a/src/data/amber_q/GAO.frg b/src/data/amber_q/GAO.frg new file mode 100644 index 0000000..4b41f1e --- /dev/null +++ b/src/data/amber_q/GAO.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$GAO + 29 1 1 0 +GAO + 1 C1 AC 3 0 0 1 1 -0.234052 0.000000 + 2 H1 H2 0 0 0 1 1 0.268381 0.000000 + 3 C2 CT 0 0 0 1 1 0.924229 0.000000 + 4 H2 H1 0 0 0 1 1 -0.165925 0.000000 + 5 N2 N 0 1 0 1 1 -0.885282 0.000000 + 6 HN2 H 0 0 0 1 1 0.397483 0.000000 + 7 C3 CT 0 0 0 1 1 0.522208 0.000000 + 8 H3 H1 0 0 0 1 1 -0.059589 0.000000 + 9 O3 OH 0 0 0 1 1 -0.361908 0.000000 + 10 HO3 HO 0 0 0 1 1 -0.304261 0.000000 + 11 C4 CT 0 0 0 1 1 -0.034542 0.000000 + 12 H4 H1 0 0 0 1 1 0.001235 0.000000 + 13 O4 OH 0 0 0 1 1 -0.744863 0.000000 + 14 HO4 HO 0 0 0 1 1 0.461838 0.000000 + 15 C5 CT 0 0 0 1 1 0.666083 0.000000 + 16 H5 H1 0 0 0 1 1 -0.125322 0.000000 + 17 O5 OH 0 0 0 1 1 -0.787861 0.000000 + 18 HO5 HO 0 0 0 1 1 0.426138 0.000000 + 19 C6 CT 0 0 0 1 1 0.430396 0.000000 + 202H6 H1 0 0 0 1 1 -0.101465 0.000000 + 213H6 H1 0 0 0 1 1 -0.062752 0.000000 + 22 O6 OH 0 0 0 1 1 -0.739757 0.000000 + 23 HO6 HO 0 0 0 1 1 0.410000 0.000000 + 24 C7 C 0 0 0 1 1 0.752726 0.000000 + 25 O7 O 0 0 0 1 1 -0.693025 0.000000 + 26 C8 CT 0 0 0 1 1 -0.157396 0.000000 + 272H8 H1 0 0 0 1 1 0.065761 0.000000 + 283H8 H1 0 0 0 1 1 0.065761 0.000000 + 294H8 H1 0 0 0 1 1 0.065761 0.000000 + 1 3 7 11 15 19 22 23 + 2 1 + 6 5 + 4 3 5 24 26 29 + 8 7 9 10 + 12 11 13 14 + 16 15 17 18 + 20 19 21 + 25 24 + 27 26 28 + diff --git a/src/data/amber_q/GC1.frg b/src/data/amber_q/GC1.frg new file mode 100644 index 0000000..d3a181b --- /dev/null +++ b/src/data/amber_q/GC1.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$GC1 + 20 1 1 0 +GC1 + 1 OR OS 0 0 0 1 1 -0.436730 0.000000 + 2 C1 AC 3 0 0 1 1 0.431092 0.000000 + 3 H1 H2 0 0 0 1 1 0.016247 0.000000 + 4 C2 CT 0 0 0 1 1 -0.182335 0.000000 + 5 H2 H1 0 0 0 1 1 0.149573 0.000000 + 6 N2 N 4 1 0 1 1 -0.341393 0.000000 + 7 HN H 0 0 0 1 1 0.236348 0.000000 + 8 C3 CT 0 0 0 1 1 0.081645 0.000000 + 9 H3 H1 0 0 0 1 1 0.037446 0.000000 + 10 O3 OS 5 0 0 1 1 -0.183535 0.000000 + 11 C4 CT 0 0 0 1 1 0.099460 0.000000 + 12 H4 H1 0 0 0 1 1 0.152421 0.000000 + 13 O4 OH 0 0 0 1 1 -0.675942 0.000000 + 14 HO HO 0 0 0 1 1 0.461259 0.000000 + 15 C5 CT 0 0 0 1 1 0.105993 0.000000 + 16 H5 H1 0 0 0 1 1 -0.010713 0.000000 + 17 C6 CT 0 0 0 1 1 0.149829 0.000000 + 182H6 H1 0 0 0 1 1 0.054121 0.000000 + 193H6 H1 0 0 0 1 1 0.054121 0.000000 + 20 O6 OG 6 0 0 1 1 -0.198907 0.000000 + 1 2 + 1 15 + 2 3 + 2 4 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/GC2.frg b/src/data/amber_q/GC2.frg new file mode 100644 index 0000000..5ca78e3 --- /dev/null +++ b/src/data/amber_q/GC2.frg @@ -0,0 +1,41 @@ +# This is an automatically generated fragment file +# +$GC2 + 18 1 1 0 +GC2 + 1 C1 AC 3 0 0 1 1 -0.132719 0.000000 + 2 H1 H2 0 0 0 1 1 0.163584 0.000000 + 3 OR OS 0 0 0 1 1 -0.201045 0.000000 + 4 C5 CT 0 0 0 1 1 -0.029468 0.000000 + 5 H5 H1 0 0 0 1 1 0.155377 0.000000 + 6 C6 CT 0 0 0 1 1 -0.048733 0.000000 + 72H6 H1 0 0 0 1 1 0.172392 0.000000 + 83H6 H1 0 0 0 1 1 0.172392 0.000000 + 9 O6 OG 4 0 0 1 1 -0.319684 0.000000 + 10 C4 CT 5 0 0 1 1 -0.205854 0.000000 + 11 H4 H1 0 0 0 1 1 0.232203 0.000000 + 12 C3 CT 0 0 0 1 1 0.142364 0.000000 + 13 H3 H1 0 0 0 1 1 0.127683 0.000000 + 14 O3 OS 6 0 0 1 1 -0.328735 0.000000 + 15 C2 CT 0 0 0 1 1 0.037713 0.000000 + 16 H2 H1 0 0 0 1 1 0.186171 0.000000 + 17 N2 N 7 1 0 1 1 -0.494259 0.000000 + 18 HN H 0 0 0 1 1 0.370618 0.000000 + 1 2 + 1 3 + 1 15 + 3 4 + 4 5 + 4 6 + 4 10 + 6 7 + 6 8 + 6 9 + 10 11 + 10 12 + 12 13 + 12 14 + 12 15 + 15 16 + 15 17 + 17 18 diff --git a/src/data/amber_q/GC2.sgm b/src/data/amber_q/GC2.sgm new file mode 100644 index 0000000..888016f --- /dev/null +++ b/src/data/amber_q/GC2.sgm @@ -0,0 +1,229 @@ +# This is an automatically generated segment file +# + 4.600000 + 18 18 32 44 0 0 1 1 + 0.000000 + 1 C1 3 0 0 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0.00000E+00 + 26 12 8 10 11 0 0 + 0 0.000000 0.00000E+00 + 27 4 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 28 4 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 29 4 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 30 9 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 31 9 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 32 9 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 33 10 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 34 10 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 35 10 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 36 8 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 37 13 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 38 16 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 39 8 12 16 1 0 0 + 0 0.000000 0.00000E+00 + 40 8 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 41 8 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 42 13 12 16 1 0 0 + 0 0.000000 0.00000E+00 + 43 13 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 44 13 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 45 14 12 16 1 0 0 + 0 0.000000 0.00000E+00 + 46 14 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 47 14 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 48 1 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 49 1 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 50 1 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 51 12 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 52 12 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 53 12 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 56 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/GCN.frg b/src/data/amber_q/GCN.frg new file mode 100644 index 0000000..f083fa4 --- /dev/null +++ b/src/data/amber_q/GCN.frg @@ -0,0 +1,61 @@ +# This is an automatically generated fragment file +# +$GCN + 28 1 1 0 +GCN + 1 C1 AC 3 0 0 1 1 -0.296859 0.000000 + 2 H1 H2 0 0 0 1 1 0.317068 0.000000 + 3 OR OS 0 0 0 1 1 -0.314059 0.000000 + 4 C2 CT 0 0 0 1 1 0.023708 0.000000 + 5 H2 H1 0 0 0 1 1 0.120847 0.000000 + 6 N2 N 0 1 0 1 1 -0.201785 0.000000 + 7 HN2 H 0 0 0 1 1 0.235695 0.000000 + 8 C7 C 0 1 0 1 1 0.402777 0.000000 + 9 O7 O 0 0 0 1 1 -0.486348 0.000000 + 10 C8 CT 0 0 0 1 1 -0.142851 0.000000 + 112H8 HC 0 0 0 1 1 0.050584 0.000000 + 123H8 HC 0 0 0 1 1 0.050584 0.000000 + 134H8 HC 0 0 0 1 1 0.050584 0.000000 + 14 C3 CT 0 0 0 1 1 -0.024602 0.000000 + 15 H3 H1 0 0 0 1 1 0.108146 0.000000 + 16 O3 OH 0 0 0 1 1 -0.623229 0.000000 + 17 HO3 HO 0 0 0 1 1 0.415358 0.000000 + 18 C4 CT 0 0 0 1 1 0.316496 0.000000 + 19 H4 H1 0 0 0 1 1 0.059330 0.000000 + 20 O4 OH 0 0 0 1 1 -0.621120 0.000000 + 21 HO4 HO 0 0 0 1 1 0.415686 0.000000 + 22 C5 CT 0 0 0 1 1 0.074395 0.000000 + 23 H5 H1 0 0 0 1 1 0.057817 0.000000 + 24 C6 CT 0 0 0 1 1 0.037971 0.000000 + 252H6 H1 0 0 0 1 1 0.097941 0.000000 + 263H6 H1 0 0 0 1 1 0.097941 0.000000 + 27 O6 OH 0 0 0 1 1 -0.558783 0.000000 + 28 HO6 HO 0 0 0 1 1 0.336708 0.000000 + 1 2 + 1 3 + 1 4 + 3 22 + 4 5 + 4 6 + 4 14 + 6 7 + 6 8 + 8 9 + 8 10 + 10 11 + 10 12 + 10 13 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 24 25 + 24 26 + 24 27 + 27 28 diff --git a/src/data/amber_q/GDP.frg b/src/data/amber_q/GDP.frg new file mode 100644 index 0000000..e524512 --- /dev/null +++ b/src/data/amber_q/GDP.frg @@ -0,0 +1,95 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are obtained from HF 6-31g* +# followed by RESP charge fitting. Charges of equivalent +# atoms are averaged +# +# GDP : Guanosine diphosphate +# +# Prepared by T.P.Straatsma 7/16/99 +# +$GDP + 40 1 1 0 +GDP + 1 PB P 0 0 0 1 1 1.074698 0.000000 + 2 O1B O2 0 0 0 1 1 -0.925822 0.000000 + 3 O2B O2 0 0 0 1 1 -0.925822 0.000000 + 4 O3B O2 0 0 0 1 1 -0.925822 0.000000 + 5 O3A OS 0 0 0 1 1 -0.343237 0.000000 + 6 PA P 0 0 0 1 1 1.174128 0.000000 + 7 O2A O2 0 0 0 1 1 -0.855657 0.000000 + 8 O1A O2 0 0 0 1 1 -0.855657 0.000000 + 9 O5* OS 0 0 0 1 1 -0.499273 0.000000 + 10 C5* CT 0 0 0 1 1 0.009374 0.000000 + 112H5* H1 0 0 0 1 1 0.101660 0.000000 + 123H5* H1 0 0 0 1 1 0.101660 0.000000 + 13 C4* CT 0 0 0 1 1 0.023226 0.000000 + 14 H4* H1 0 0 0 1 1 0.053000 0.000000 + 15 O4* OS 0 0 0 1 1 -0.393256 0.000000 + 16 C3* CT 0 0 0 1 1 0.471263 0.000000 + 17 H3* H1 0 0 0 1 1 0.036811 0.000000 + 18 O3* OH 0 0 0 1 1 -0.755512 0.000000 + 19 HO3 HO 0 0 0 1 1 0.387701 0.000000 + 20 C2* CT 0 0 0 1 1 0.149357 0.000000 + 21 H2* H1 0 0 0 1 1 0.138958 0.000000 + 22 O2* OH 0 0 0 1 1 -0.688406 0.000000 + 23 HO2 HO 0 0 0 1 1 0.409882 0.000000 + 24 C1* CT 0 0 0 1 1 0.117387 0.000000 + 25 H1* H2 0 0 0 1 1 0.099402 0.000000 + 26 N9 N* 0 5 0 1 1 -0.064859 0.000000 + 27 C8 CK 0 5 0 1 1 0.240444 0.000000 + 28 H8 H5 0 0 0 1 1 0.171277 0.000000 + 29 N7 NB 0 5 0 1 1 -0.575569 0.000000 + 30 C5 CB 0 11 0 1 1 0.203252 0.000000 + 31 C6 C 0 6 0 1 1 0.460522 0.000000 + 32 O6 O 0 0 0 1 1 -0.625150 0.000000 + 33 N1 NA 0 6 0 1 1 -0.469413 0.000000 + 34 H1 H 0 0 0 1 1 0.321419 0.000000 + 35 C2 CA 0 6 0 1 1 0.818564 0.000000 + 362H2 H 0 0 0 1 1 0.448190 0.000000 + 373H2 H 0 0 0 1 1 0.448190 0.000000 + 38 N2 N2 0 1 0 1 1 -1.107937 0.000000 + 39 N3 NC 0 6 0 1 1 -0.626702 0.000000 + 40 C4 CB 0 11 0 1 1 0.177729 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 + 15 24 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 24 + 22 23 + 24 25 + 24 26 + 26 27 + 26 40 + 27 28 + 27 29 + 29 30 + 30 31 + 30 40 + 31 32 + 31 33 + 33 34 + 33 35 + 35 38 + 35 39 + 36 38 + 37 38 + 39 40 diff --git a/src/data/amber_q/GL1.frg b/src/data/amber_q/GL1.frg new file mode 100644 index 0000000..6aa373b --- /dev/null +++ b/src/data/amber_q/GL1.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$GL1 + 20 1 1 0 +GL1 + 1 C1 AC 3 0 0 1 1 -0.005309 0.000000 + 2 H1 H2 0 0 0 1 1 0.265099 0.000000 + 3 OR OS 0 0 0 1 1 -0.487694 0.000000 + 4 C2 CT 0 0 0 1 1 0.121052 0.000000 + 5 H2 H1 0 0 0 1 1 0.203257 0.000000 + 6 O2 OH 0 0 0 1 1 -0.767877 0.000000 + 7 HO2 HO 0 0 0 1 1 0.584113 0.000000 + 8 C3 CT 0 0 0 1 1 -0.001486 0.000000 + 9 H3 H1 0 0 0 1 1 0.160825 0.000000 + 10 O3 OG 4 0 0 1 1 -0.333535 0.000000 + 11 C4 CT 0 0 0 1 1 0.071732 0.000000 + 12 H4 H1 0 0 0 1 1 0.107505 0.000000 + 13 O4 OH 0 0 0 1 1 -0.571075 0.000000 + 14 HO4 HO 0 0 0 1 1 0.450311 0.000000 + 15 C5 CT 0 0 0 1 1 0.035653 0.000000 + 16 H5 H1 0 0 0 1 1 0.086102 0.000000 + 17 C6 CT 0 0 0 1 1 0.074859 0.000000 + 182H6 H1 0 0 0 1 1 0.106383 0.000000 + 193H6 H1 0 0 0 1 1 0.106383 0.000000 + 20 O6 OG 5 0 0 1 1 -0.206298 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/GL2.frg b/src/data/amber_q/GL2.frg new file mode 100644 index 0000000..2c76048 --- /dev/null +++ b/src/data/amber_q/GL2.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$GL2 + 20 1 1 0 +GL2 + 1 C1 AC 3 0 0 1 1 -0.014294 0.000000 + 2 H1 H2 0 0 0 1 1 0.209438 0.000000 + 3 OR OS 0 0 0 1 1 -0.343306 0.000000 + 4 C2 CT 0 0 0 1 1 -0.035484 0.000000 + 5 H2 H1 0 0 0 1 1 0.172160 0.000000 + 6 O2 OG 4 0 0 1 1 -0.221659 0.000000 + 7 C3 CT 0 0 0 1 1 0.020232 0.000000 + 8 H3 H1 0 0 0 1 1 0.174479 0.000000 + 9 O3 OH 0 0 0 1 1 -0.597323 0.000000 + 10 HO3 HO 0 0 0 1 1 0.448165 0.000000 + 11 C4 CT 0 0 0 1 1 0.018125 0.000000 + 12 H4 H1 0 0 0 1 1 0.148347 0.000000 + 13 O4 OG 5 0 0 1 1 -0.154442 0.000000 + 14 C5 CT 0 0 0 1 1 0.079364 0.000000 + 15 H5 H1 0 0 0 1 1 0.099999 0.000000 + 16 C6 CT 0 0 0 1 1 -0.040044 0.000000 + 172H6 H1 0 0 0 1 1 0.115179 0.000000 + 183H6 H1 0 0 0 1 1 0.115179 0.000000 + 19 O6 OH 0 0 0 1 1 -0.638046 0.000000 + 20 HO6 HO 0 0 0 1 1 0.443931 0.000000 + 1 2 + 1 3 + 1 4 + 3 14 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 16 17 + 16 18 + 16 19 + 19 20 diff --git a/src/data/amber_q/GL3.frg b/src/data/amber_q/GL3.frg new file mode 100644 index 0000000..7977946 --- /dev/null +++ b/src/data/amber_q/GL3.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# +$GL3 + 22 1 1 0 +GL3 + 1 C1 AC 3 0 0 1 1 -0.180893 0.000000 + 2 H1 H2 0 0 0 1 1 0.208778 0.000000 + 3 C2 CT 0 0 0 1 1 0.125803 0.000000 + 4 H2 H1 0 0 0 1 1 0.141710 0.000000 + 5 O2 OH 0 0 0 1 1 -0.611123 0.000000 + 6 HO2 HO 0 0 0 1 1 0.351163 0.000000 + 7 C3 CT 0 0 0 1 1 0.260857 0.000000 + 8 H3 H1 0 0 0 1 1 0.032562 0.000000 + 9 O3 OH 0 0 0 1 1 -0.666787 0.000000 + 10 HO3 HO 0 0 0 1 1 0.430357 0.000000 + 11 C4 CT 0 0 0 1 1 0.082532 0.000000 + 12 H4 H1 0 0 0 1 1 0.086780 0.000000 + 13 O4 OH 0 0 0 1 1 -0.646332 0.000000 + 14 HO4 HO 0 0 0 1 1 0.431530 0.000000 + 15 C5 CT 0 0 0 1 1 0.035447 0.000000 + 16 H5 H1 0 0 0 1 1 0.134125 0.000000 + 17 OR OS 0 0 0 1 1 -0.235957 0.000000 + 18 C6 CT 0 0 0 1 1 0.103632 0.000000 + 192H6 H1 0 0 0 1 1 0.074155 0.000000 + 203H6 H1 0 0 0 1 1 0.074155 0.000000 + 21 O6 OH 0 0 0 1 1 -0.668207 0.000000 + 22 HO6 HO 0 0 0 1 1 0.435713 0.000000 + 1 2 + 1 3 + 1 17 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 15 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GL4.frg b/src/data/amber_q/GL4.frg new file mode 100644 index 0000000..5377d35 --- /dev/null +++ b/src/data/amber_q/GL4.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL4 + 21 1 1 0 +GL4 + 1 C1 EC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 0 1 1 0.050000 0.000000 + 21 O6 OG 4 0 0 1 1 -0.300000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 diff --git a/src/data/amber_q/GL4.sgm b/src/data/amber_q/GL4.sgm new file mode 100644 index 0000000..2cad33b --- /dev/null +++ b/src/data/amber_q/GL4.sgm @@ -0,0 +1,275 @@ +# This is an automatically generated segment file +# + 4.600000 + 21 21 37 56 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + EC 0.041291 0.000000 + 2 H1 0 0 0 1 1 + H2 0.170645 0.000000 + 3 OR 0 0 0 1 1 + OS -0.365330 0.000000 + 4 C2 0 0 0 1 1 + CT 0.081809 0.000000 + 5 H2 0 0 0 1 1 + H1 0.162189 0.000000 + 6 O2 0 0 0 1 1 + OH -0.599983 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.340524 0.000000 + 8 C3 0 0 0 1 1 + CT 0.078232 0.000000 + 9 H3 0 0 0 1 1 + H1 0.160184 0.000000 + 10 O3 0 0 0 1 1 + OH -0.605072 0.000000 + 11 HO3 0 0 0 1 1 + HO 0.409833 0.000000 + 12 C4 0 0 0 1 1 + CT 0.095775 0.000000 + 13 H4 0 0 0 1 1 + H1 0.136486 0.000000 + 14 O4 0 0 0 1 1 + OH -0.634070 0.000000 + 15 HO4 0 0 0 1 1 + HO 0.467736 0.000000 + 16 C5 0 0 0 1 1 + CT 0.010339 0.000000 + 17 H5 0 0 0 1 1 + H1 0.151057 0.000000 + 18 C6 0 0 0 1 1 + CT -0.014409 0.000000 + 192H6 0 0 0 1 1 + H1 0.104895 0.000000 + 203H6 0 0 0 1 1 + H1 0.104895 0.000000 + 21 O6 4 0 0 1 1 + OG -0.297026 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 16 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 8 0 0 + 0.000000 0.00000E+00 + 8 6 7 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 8 10 0 0 + 0.000000 0.00000E+00 + 11 8 12 0 0 + 0.000000 0.00000E+00 + 12 10 11 0 0 + 0.000000 0.00000E+00 + 13 12 13 0 0 + 0.000000 0.00000E+00 + 14 12 14 0 0 + 0.000000 0.00000E+00 + 15 12 16 0 0 + 0.000000 0.00000E+00 + 16 14 15 0 0 + 0.000000 0.00000E+00 + 17 16 17 0 0 + 0.000000 0.00000E+00 + 18 16 18 0 0 + 0.000000 0.00000E+00 + 19 18 19 0 0 + 0.000000 0.00000E+00 + 20 18 20 0 0 + 0.000000 0.00000E+00 + 21 18 21 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 3 16 0 0 + 0.000000 0.00000E+00 + 5 1 4 5 0 0 + 0.000000 0.00000E+00 + 6 1 4 6 0 0 + 0.000000 0.00000E+00 + 7 1 4 8 0 0 + 0.000000 0.00000E+00 + 8 5 4 6 0 0 + 0.000000 0.00000E+00 + 9 5 4 8 0 0 + 0.000000 0.00000E+00 + 10 6 4 8 0 0 + 0.000000 0.00000E+00 + 11 4 6 7 0 0 + 0.000000 0.00000E+00 + 12 4 8 9 0 0 + 0.000000 0.00000E+00 + 13 4 8 10 0 0 + 0.000000 0.00000E+00 + 14 4 8 12 0 0 + 0.000000 0.00000E+00 + 15 9 8 10 0 0 + 0.000000 0.00000E+00 + 16 9 8 12 0 0 + 0.000000 0.00000E+00 + 17 10 8 12 0 0 + 0.000000 0.00000E+00 + 18 8 10 11 0 0 + 0.000000 0.00000E+00 + 19 8 12 13 0 0 + 0.000000 0.00000E+00 + 20 8 12 14 0 0 + 0.000000 0.00000E+00 + 21 8 12 16 0 0 + 0.000000 0.00000E+00 + 22 13 12 14 0 0 + 0.000000 0.00000E+00 + 23 13 12 16 0 0 + 0.000000 0.00000E+00 + 24 14 12 16 0 0 + 0.000000 0.00000E+00 + 25 12 14 15 0 0 + 0.000000 0.00000E+00 + 26 3 16 12 0 0 + 0.000000 0.00000E+00 + 27 3 16 17 0 0 + 0.000000 0.00000E+00 + 28 3 16 18 0 0 + 0.000000 0.00000E+00 + 29 12 16 17 0 0 + 0.000000 0.00000E+00 + 30 12 16 18 0 0 + 0.000000 0.00000E+00 + 31 17 16 18 0 0 + 0.000000 0.00000E+00 + 32 16 18 19 0 0 + 0.000000 0.00000E+00 + 33 16 18 20 0 0 + 0.000000 0.00000E+00 + 34 16 18 21 0 0 + 0.000000 0.00000E+00 + 35 19 18 20 0 0 + 0.000000 0.00000E+00 + 36 19 18 21 0 0 + 0.000000 0.00000E+00 + 37 20 18 21 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 16 0 0 + 0 0.000000 0.00000E+00 + 2 4 1 3 16 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 4 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 5 2 1 4 8 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 7 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 8 3 1 4 8 0 0 + 0 0.000000 0.00000E+00 + 9 1 3 16 12 0 0 + 0 0.000000 0.00000E+00 + 10 1 3 16 17 0 0 + 0 0.000000 0.00000E+00 + 11 1 3 16 18 0 0 + 0 0.000000 0.00000E+00 + 12 1 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 13 5 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 14 8 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 15 1 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 16 1 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 17 1 4 8 12 0 0 + 0 0.000000 0.00000E+00 + 18 5 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 19 5 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 20 5 4 8 12 0 0 + 0 0.000000 0.00000E+00 + 21 6 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 22 6 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 23 6 4 8 12 0 0 + 0 0.000000 0.00000E+00 + 24 4 8 10 11 0 0 + 0 0.000000 0.00000E+00 + 25 9 8 10 11 0 0 + 0 0.000000 0.00000E+00 + 26 12 8 10 11 0 0 + 0 0.000000 0.00000E+00 + 27 4 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 28 4 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 29 4 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 30 9 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 31 9 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 32 9 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 33 10 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 34 10 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 35 10 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 36 8 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 37 13 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 38 16 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 39 8 12 16 3 0 0 + 0 0.000000 0.00000E+00 + 40 8 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 41 8 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 42 13 12 16 3 0 0 + 0 0.000000 0.00000E+00 + 43 13 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 44 13 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 45 14 12 16 3 0 0 + 0 0.000000 0.00000E+00 + 46 14 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 47 14 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 48 3 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 49 3 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 50 3 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 51 12 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 52 12 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 53 12 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 56 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/GL5.frg b/src/data/amber_q/GL5.frg new file mode 100644 index 0000000..fe2e89c --- /dev/null +++ b/src/data/amber_q/GL5.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL5 + 22 1 1 0 +GL5 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 0 1 1 0.050000 0.000000 + 21 O6 OH 0 0 0 1 1 -0.490000 0.000000 + 22 HO6 HO 0 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GL5.sgm b/src/data/amber_q/GL5.sgm new file mode 100644 index 0000000..9451803 --- /dev/null +++ b/src/data/amber_q/GL5.sgm @@ -0,0 +1,287 @@ +# This is an automatically generated segment file +# + 4.600000 + 22 22 38 59 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC -0.065653 0.000000 + 2 H1 0 0 0 1 1 + H2 0.131822 0.000000 + 3 OR 0 0 0 1 1 + OS -0.318121 0.000000 + 4 C2 0 0 0 1 1 + CT 0.211162 0.000000 + 5 H2 0 0 0 1 1 + H1 0.123548 0.000000 + 6 O2 0 0 0 1 1 + OH -0.717988 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.475195 0.000000 + 8 C3 0 0 0 1 1 + CT 0.148320 0.000000 + 9 H3 0 0 0 1 1 + H1 0.086125 0.000000 + 10 O3 0 0 0 1 1 + OH -0.699269 0.000000 + 11 HO3 0 0 0 1 1 + HO 0.462868 0.000000 + 12 C4 0 0 0 1 1 + CT 0.142201 0.000000 + 13 H4 0 0 0 1 1 + H1 0.083287 0.000000 + 14 O4 0 0 0 1 1 + OH -0.685786 0.000000 + 15 HO4 0 0 0 1 1 + HO 0.444588 0.000000 + 16 C5 0 0 0 1 1 + CT 0.045211 0.000000 + 17 H5 0 0 0 1 1 + H1 0.105169 0.000000 + 18 C6 0 0 0 1 1 + CT 0.147800 0.000000 + 192H6 0 0 0 1 1 + H1 0.066265 0.000000 + 203H6 0 0 0 1 1 + H1 0.066265 0.000000 + 21 O6 0 0 0 1 1 + OH -0.680062 0.000000 + 22 HO6 0 0 0 1 1 + HO 0.427053 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 16 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 8 0 0 + 0.000000 0.00000E+00 + 8 6 7 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 8 10 0 0 + 0.000000 0.00000E+00 + 11 8 12 0 0 + 0.000000 0.00000E+00 + 12 10 11 0 0 + 0.000000 0.00000E+00 + 13 12 13 0 0 + 0.000000 0.00000E+00 + 14 12 14 0 0 + 0.000000 0.00000E+00 + 15 12 16 0 0 + 0.000000 0.00000E+00 + 16 14 15 0 0 + 0.000000 0.00000E+00 + 17 16 17 0 0 + 0.000000 0.00000E+00 + 18 16 18 0 0 + 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0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 56 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 57 16 18 21 22 0 0 + 0 0.000000 0.00000E+00 + 58 19 18 21 22 0 0 + 0 0.000000 0.00000E+00 + 59 20 18 21 22 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/GL6.frg b/src/data/amber_q/GL6.frg new file mode 100644 index 0000000..9164061 --- /dev/null +++ b/src/data/amber_q/GL6.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL6 + 21 1 1 0 +GL6 + 1 C1 EC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 19 O6 OG 4 0 0 1 1 -0.300000 0.000000 + 202H6 H1 0 0 0 1 1 0.050000 0.000000 + 213H6 H1 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 diff --git a/src/data/amber_q/GL6.sgm b/src/data/amber_q/GL6.sgm new file mode 100644 index 0000000..36522f9 --- /dev/null +++ b/src/data/amber_q/GL6.sgm @@ -0,0 +1,275 @@ +# This is an automatically generated segment file +# + 4.600000 + 21 21 37 56 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + EC 0.043199 0.000000 + 2 H1 0 0 0 1 1 + H2 0.105035 0.000000 + 3 OR 0 0 0 1 1 + OS -0.392286 0.000000 + 4 C2 0 0 0 1 1 + CT 0.117381 0.000000 + 5 H2 0 0 0 1 1 + H1 0.243077 0.000000 + 6 O2 0 0 0 1 1 + OH -0.675882 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.459648 0.000000 + 8 C3 0 0 0 1 1 + CT 0.019740 0.000000 + 9 H3 0 0 0 1 1 + H1 0.176308 0.000000 + 10 O3 0 0 0 1 1 + OH -0.657083 0.000000 + 11 HO3 0 0 0 1 1 + HO 0.372827 0.000000 + 12 C4 0 0 0 1 1 + CT 0.140436 0.000000 + 13 H4 0 0 0 1 1 + H1 0.080082 0.000000 + 14 O4 0 0 0 1 1 + OH -0.706987 0.000000 + 15 HO4 0 0 0 1 1 + HO 0.461415 0.000000 + 16 C5 0 0 0 1 1 + CT 0.154353 0.000000 + 17 H5 0 0 0 1 1 + H1 0.018973 0.000000 + 18 C6 0 0 0 1 1 + CT 0.064664 0.000000 + 19 O6 4 0 0 1 1 + OG -0.168660 0.000000 + 202H6 0 0 0 1 1 + H1 0.071880 0.000000 + 213H6 0 0 0 1 1 + H1 0.071880 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 16 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 8 0 0 + 0.000000 0.00000E+00 + 8 6 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9 8 10 11 0 0 + 0 0.000000 0.00000E+00 + 26 12 8 10 11 0 0 + 0 0.000000 0.00000E+00 + 27 4 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 28 4 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 29 4 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 30 9 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 31 9 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 32 9 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 33 10 8 12 13 0 0 + 0 0.000000 0.00000E+00 + 34 10 8 12 14 0 0 + 0 0.000000 0.00000E+00 + 35 10 8 12 16 0 0 + 0 0.000000 0.00000E+00 + 36 8 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 37 13 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 38 16 12 14 15 0 0 + 0 0.000000 0.00000E+00 + 39 8 12 16 3 0 0 + 0 0.000000 0.00000E+00 + 40 8 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 41 8 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 42 13 12 16 3 0 0 + 0 0.000000 0.00000E+00 + 43 13 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 44 13 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 45 14 12 16 3 0 0 + 0 0.000000 0.00000E+00 + 46 14 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 47 14 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 48 3 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 49 3 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 50 3 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 51 12 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 52 12 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 53 12 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 56 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/GL7.frg b/src/data/amber_q/GL7.frg new file mode 100644 index 0000000..d426122 --- /dev/null +++ b/src/data/amber_q/GL7.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL7 + 22 1 1 0 +GL7 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 0 1 1 0.050000 0.000000 + 21 O6 OH 0 0 0 1 1 -0.490000 0.000000 + 22 HO6 HO 0 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GL7.sgm b/src/data/amber_q/GL7.sgm new file mode 100644 index 0000000..875689d --- /dev/null +++ b/src/data/amber_q/GL7.sgm @@ -0,0 +1,287 @@ +# This is an automatically generated segment file +# + 4.600000 + 22 22 38 59 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC 0.030888 0.000000 + 2 H1 0 0 0 1 1 + H2 0.175753 0.000000 + 3 OR 0 0 0 1 1 + OS -0.493642 0.000000 + 4 C2 0 0 0 1 1 + CT 0.183712 0.000000 + 5 H2 0 0 0 1 1 + H1 0.071613 0.000000 + 6 O2 0 0 0 1 1 + OH -0.661663 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.439450 0.000000 + 8 C3 0 0 0 1 1 + CT 0.297712 0.000000 + 9 H3 0 0 0 1 1 + H1 0.035153 0.000000 + 10 O3 0 0 0 1 1 + OH -0.718691 0.000000 + 11 HO3 0 0 0 1 1 + HO 0.429136 0.000000 + 12 C4 0 0 0 1 1 + CT 0.045111 0.000000 + 13 H4 0 0 0 1 1 + H1 0.084908 0.000000 + 14 O4 0 0 0 1 1 + OH -0.648695 0.000000 + 15 HO4 0 0 0 1 1 + HO 0.421719 0.000000 + 16 C5 0 0 0 1 1 + CT 0.126032 0.000000 + 17 H5 0 0 0 1 1 + H1 0.130527 0.000000 + 18 C6 0 0 0 1 1 + CT 0.258980 0.000000 + 192H6 0 0 0 1 1 + H1 0.034407 0.000000 + 203H6 0 0 0 1 1 + H1 0.034407 0.000000 + 21 O6 0 0 0 1 1 + OH -0.687752 0.000000 + 22 HO6 0 0 0 1 1 + HO 0.410935 0.000000 + 1 1 2 0 0 + 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18 0 0 + 0 0.000000 0.00000E+00 + 48 3 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 49 3 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 50 3 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 51 12 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 52 12 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 53 12 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 56 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 57 16 18 21 22 0 0 + 0 0.000000 0.00000E+00 + 58 19 18 21 22 0 0 + 0 0.000000 0.00000E+00 + 59 20 18 21 22 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/GNP.frg b/src/data/amber_q/GNP.frg new file mode 100644 index 0000000..4616dff --- /dev/null +++ b/src/data/amber_q/GNP.frg @@ -0,0 +1,105 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are obtained from HF 6-31g* +# followed by RESP charge fitting. Charges of equivalent +# atoms are averaged +# +# GNP : Guanosine imido triphosphate +# +# Prepared by T.P.Straatsma 7/16/99 +# +$GNP + 45 1 1 0 +GNP + 1 PG P 0 0 0 1 1 1.096457 0.000000 + 2 O1G O2 0 0 0 1 1 -0.940148 0.000000 + 3 O2G O2 0 0 0 1 1 -0.940148 0.000000 + 4 O3G O2 0 0 0 1 1 -0.940148 0.000000 + 5 N3B N 0 0 0 1 1 -0.769579 0.000000 + 6 H3B H 0 0 0 1 1 0.315452 0.000000 + 7 PB P 0 0 0 1 1 1.243377 0.000000 + 8 O1B O2 0 0 0 1 1 -0.843182 0.000000 + 9 O2B O2 0 0 0 1 1 -0.843182 0.000000 + 10 O3A OS 0 0 0 1 1 -0.474613 0.000000 + 11 PA P 0 0 0 1 1 1.171633 0.000000 + 12 O2A O2 0 0 0 1 1 -0.843894 0.000000 + 13 O1A O2 0 0 0 1 1 -0.843894 0.000000 + 14 O5* OS 0 0 0 1 1 -0.451770 0.000000 + 15 C5* CT 0 0 0 1 1 0.008623 0.000000 + 162H5* H1 0 0 0 1 1 0.104767 0.000000 + 173H5* H1 0 0 0 1 1 0.104767 0.000000 + 18 C4* CT 0 0 0 1 1 -0.005814 0.000000 + 19 H4* H1 0 0 0 1 1 0.061627 0.000000 + 20 O4* OS 0 0 0 1 1 -0.391274 0.000000 + 21 C3* CT 0 0 0 1 1 0.491472 0.000000 + 22 H3* H1 0 0 0 1 1 0.024986 0.000000 + 23 O3* OH 0 0 0 1 1 -0.753126 0.000000 + 24 HO3 HO 0 0 0 1 1 0.385926 0.000000 + 25 C2* CT 0 0 0 1 1 0.152716 0.000000 + 26 H2* H1 0 0 0 1 1 0.132748 0.000000 + 27 O2* OH 0 0 0 1 1 -0.686327 0.000000 + 28 HO2 HO 0 0 0 1 1 0.404134 0.000000 + 29 C1* CT 0 0 0 1 1 0.113955 0.000000 + 30 H1* H2 0 0 0 1 1 0.100141 0.000000 + 31 N9 N* 0 5 0 1 1 -0.068035 0.000000 + 32 C8 CK 0 5 0 1 1 0.241741 0.000000 + 33 H8 H5 0 0 0 1 1 0.173878 0.000000 + 34 N7 NB 0 5 0 1 1 -0.572419 0.000000 + 35 C5 CB 0 11 0 1 1 0.197931 0.000000 + 36 C6 C 0 6 0 1 1 0.464446 0.000000 + 37 O6 O 0 0 0 1 1 -0.629089 0.000000 + 38 N1 NA 0 6 0 1 1 -0.474110 0.000000 + 39 H1 H 0 0 0 1 1 0.320584 0.000000 + 40 C2 CA 0 6 0 1 1 0.821048 0.000000 + 412H2 H 0 0 0 1 1 0.446735 0.000000 + 423H2 H 0 0 0 1 1 0.446735 0.000000 + 43 N2 N2 0 1 0 1 1 -1.110790 0.000000 + 44 N3 NC 0 6 0 1 1 -0.627045 0.000000 + 45 C4 CB 0 11 0 1 1 0.182708 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 7 8 + 7 9 + 7 10 + 10 11 + 11 12 + 11 13 + 11 14 + 14 15 + 15 16 + 15 17 + 15 18 + 18 19 + 18 20 + 18 21 + 20 29 + 21 22 + 21 23 + 21 25 + 23 24 + 25 26 + 25 27 + 25 29 + 27 28 + 29 30 + 29 31 + 31 32 + 31 45 + 32 33 + 32 34 + 34 35 + 35 36 + 35 45 + 36 37 + 36 38 + 38 39 + 38 40 + 40 43 + 40 44 + 41 43 + 42 43 + 44 45 diff --git a/src/data/amber_q/GTL.sgm b/src/data/amber_q/GTL.sgm new file mode 100644 index 0000000..288c5b1 --- /dev/null +++ b/src/data/amber_q/GTL.sgm @@ -0,0 +1,401 @@ +# This is an automatically generated segment file +# + 4.600000 + 30 30 56 81 1 0 1 1 + 0.000000 + 1 C1 0 0 0 1 1 + CT 0.038921 0.000000 + 22H1 0 0 0 1 1 + H1 0.186521 0.000000 + 33H1 0 0 0 1 1 + H1 0.000000 0.000000 + 4 OR 0 0 0 1 1 + OS -0.369500 0.000000 + 5 C2 0 0 0 1 1 + CT 0.088495 0.000000 + 6 H2 0 0 0 1 1 + H1 0.128159 0.000000 + 7 C3 0 0 0 1 1 + CT -0.003142 0.000000 + 8 H3 0 0 0 1 1 + H1 0.070396 0.000000 + 9 O3 3 0 0 1 1 + OS -0.202001 0.000000 + 10 C4 0 0 0 1 1 + CT 0.054364 0.000000 + 11 H4 0 0 0 1 1 + H1 0.123615 0.000000 + 12 O4 4 0 0 1 1 + OS -0.141163 0.000000 + 13 C5 0 0 0 1 1 + CT 0.132859 0.000000 + 14 H5 0 0 0 1 1 + H1 0.042566 0.000000 + 15 C6 0 0 0 1 1 + CT 0.015802 0.000000 + 162H6 0 0 0 1 1 + H1 0.084992 0.000000 + 173H6 0 0 0 1 1 + H1 0.084992 0.000000 + 18 O6 0 0 0 1 1 + OH -0.590914 0.000000 + 19 HO6 0 0 0 1 1 + HO 0.367747 0.000000 + 20 N 0 0 0 1 1 + N -0.492386 0.000000 + 21 HN 0 0 0 1 1 + H 0.238725 0.000000 + 22 CA 0 0 0 1 1 + CT 0.086698 0.000000 + 23 HA 0 0 0 1 1 + H1 0.054254 0.000000 + 24 CB 0 0 0 1 1 + CT -0.300000 0.000000 + 252HB 0 0 0 1 1 + HC 0.100000 0.000000 + 263HB 0 0 0 1 1 + HC 0.100000 0.000000 + 274HB 0 0 0 1 1 + HC 0.100000 0.000000 + 28 C 0 1 0 1 1 + C 0.586128 0.000000 + 29 OC 0 0 0 1 1 + O2 -0.793064 0.000000 + 30 O 0 0 0 1 1 + O2 -0.793064 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 4 13 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 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0.000000 0.00000E+00 + 22 20 5 7 8 0 0 + 0 0.000000 0.00000E+00 + 23 20 5 7 9 0 0 + 0 0.000000 0.00000E+00 + 24 20 5 7 10 0 0 + 0 0.000000 0.00000E+00 + 25 1 5 20 21 0 0 + 0 0.000000 0.00000E+00 + 26 1 5 20 22 0 0 + 0 0.000000 0.00000E+00 + 27 6 5 20 21 0 0 + 0 0.000000 0.00000E+00 + 28 6 5 20 22 0 0 + 0 0.000000 0.00000E+00 + 29 7 5 20 21 0 0 + 0 0.000000 0.00000E+00 + 30 7 5 20 22 0 0 + 0 0.000000 0.00000E+00 + 31 5 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 32 5 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 33 5 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 34 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 35 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 36 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 37 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 38 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 39 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 40 7 10 13 4 0 0 + 0 0.000000 0.00000E+00 + 41 7 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 42 7 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 43 11 10 13 4 0 0 + 0 0.000000 0.00000E+00 + 44 11 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 45 11 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 46 12 10 13 4 0 0 + 0 0.000000 0.00000E+00 + 47 12 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 48 12 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 49 4 13 15 16 0 0 + 0 0.000000 0.00000E+00 + 50 4 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 51 4 13 15 18 0 0 + 0 0.000000 0.00000E+00 + 52 10 13 15 16 0 0 + 0 0.000000 0.00000E+00 + 53 10 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 54 10 13 15 18 0 0 + 0 0.000000 0.00000E+00 + 55 14 13 15 16 0 0 + 0 0.000000 0.00000E+00 + 56 14 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 57 14 13 15 18 0 0 + 0 0.000000 0.00000E+00 + 58 13 15 18 19 0 0 + 0 0.000000 0.00000E+00 + 59 16 15 18 19 0 0 + 0 0.000000 0.00000E+00 + 60 17 15 18 19 0 0 + 0 0.000000 0.00000E+00 + 61 5 20 22 23 0 0 + 0 0.000000 0.00000E+00 + 62 5 20 22 24 0 0 + 0 0.000000 0.00000E+00 + 63 5 20 22 28 0 0 + 0 0.000000 0.00000E+00 + 64 21 20 22 23 0 0 + 0 0.000000 0.00000E+00 + 65 21 20 22 24 0 0 + 0 0.000000 0.00000E+00 + 66 21 20 22 28 0 0 + 0 0.000000 0.00000E+00 + 67 20 22 24 25 0 0 + 0 0.000000 0.00000E+00 + 68 20 22 24 26 0 0 + 0 0.000000 0.00000E+00 + 69 20 22 24 27 0 0 + 0 0.000000 0.00000E+00 + 70 23 22 24 25 0 0 + 0 0.000000 0.00000E+00 + 71 23 22 24 26 0 0 + 0 0.000000 0.00000E+00 + 72 23 22 24 27 0 0 + 0 0.000000 0.00000E+00 + 73 28 22 24 25 0 0 + 0 0.000000 0.00000E+00 + 74 28 22 24 26 0 0 + 0 0.000000 0.00000E+00 + 75 28 22 24 27 0 0 + 0 0.000000 0.00000E+00 + 76 20 22 28 29 0 0 + 0 0.000000 0.00000E+00 + 77 20 22 28 30 0 0 + 0 0.000000 0.00000E+00 + 78 23 22 28 29 0 0 + 0 0.000000 0.00000E+00 + 79 23 22 28 30 0 0 + 0 0.000000 0.00000E+00 + 80 24 22 28 29 0 0 + 0 0.000000 0.00000E+00 + 81 24 22 28 30 0 0 + 0 0.000000 0.00000E+00 + 1 22 29 28 30 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/GTP.frg b/src/data/amber_q/GTP.frg new file mode 100644 index 0000000..16413da --- /dev/null +++ b/src/data/amber_q/GTP.frg @@ -0,0 +1,103 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are obtained from HF 6-31g* +# followed by RESP charge fitting. Charges of equivalent +# atoms are averaged +# +# GTP : Guanosine triphosphate +# +# Prepared by T.P.Straatsma 7/16/99 +# +$GTP + 44 1 1 0 +GTP + 1 PG P 0 0 0 1 1 1.164170 0.000000 + 2 O1G O2 0 0 0 1 1 -0.945487 0.000000 + 3 O2G O2 0 0 0 1 1 -0.945487 0.000000 + 4 O3G O2 0 0 0 1 1 -0.945487 0.000000 + 5 PB P 0 0 0 1 1 1.240313 0.000000 + 6 O1B O2 0 0 0 1 1 -0.832996 0.000000 + 7 O2B O2 0 0 0 1 1 -0.832996 0.000000 + 8 O3B OS 0 0 0 1 1 -0.563773 0.000000 + 9 O3A OS 0 0 0 1 1 -0.420057 0.000000 + 10 PA P 0 0 0 1 1 1.145727 0.000000 + 11 O2A O2 0 0 0 1 1 -0.834828 0.000000 + 12 O1A O2 0 0 0 1 1 -0.834828 0.000000 + 13 O5* OS 0 0 0 1 1 -0.473116 0.000000 + 14 C5* CT 0 0 0 1 1 0.012341 0.000000 + 152H5* H1 0 0 0 1 1 0.107078 0.000000 + 163H5* H1 0 0 0 1 1 0.107078 0.000000 + 17 C4* CT 0 0 0 1 1 0.003260 0.000000 + 18 H4* H1 0 0 0 1 1 0.058872 0.000000 + 19 O4* OS 0 0 0 1 1 -0.395391 0.000000 + 20 C3* CT 0 0 0 1 1 0.503736 0.000000 + 21 H3* H1 0 0 0 1 1 0.024579 0.000000 + 22 O3* OH 0 0 0 1 1 -0.757441 0.000000 + 23 HO3 HO 0 0 0 1 1 0.386486 0.000000 + 24 C2* CT 0 0 0 1 1 0.136824 0.000000 + 25 H2* H1 0 0 0 1 1 0.141068 0.000000 + 26 O2* OH 0 0 0 1 1 -0.687513 0.000000 + 27 HO2 HO 0 0 0 1 1 0.405987 0.000000 + 28 C1* CT 0 0 0 1 1 0.119399 0.000000 + 29 H1* H2 0 0 0 1 1 0.098283 0.000000 + 30 N9 N* 0 5 0 1 1 -0.065470 0.000000 + 31 C8 CK 0 5 0 1 1 0.242292 0.000000 + 32 H8 H5 0 0 0 1 1 0.173702 0.000000 + 33 N7 NB 0 5 0 1 1 -0.574845 0.000000 + 34 C5 CB 0 11 0 1 1 0.199400 0.000000 + 35 C6 C 0 6 0 1 1 0.463943 0.000000 + 36 O6 O 0 0 0 1 1 -0.629076 0.000000 + 37 N1 NA 0 6 0 1 1 -0.474598 0.000000 + 38 H1 H 0 0 0 1 1 0.320504 0.000000 + 39 C2 CA 0 6 0 1 1 0.821481 0.000000 + 402H2 H 0 0 0 1 1 0.446858 0.000000 + 413H2 H 0 0 0 1 1 0.446858 0.000000 + 42 N2 N2 0 1 0 1 1 -1.111040 0.000000 + 43 N3 NC 0 6 0 1 1 -0.626706 0.000000 + 44 C4 CB 0 11 0 1 1 0.180896 0.000000 + 1 2 + 1 3 + 1 4 + 1 8 + 5 6 + 5 7 + 5 8 + 5 9 + 9 10 + 10 11 + 10 12 + 10 13 + 13 14 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 + 19 28 + 20 21 + 20 22 + 20 24 + 22 23 + 24 25 + 24 26 + 24 28 + 26 27 + 28 29 + 28 30 + 30 31 + 30 44 + 31 32 + 31 33 + 33 34 + 34 35 + 34 44 + 35 36 + 35 37 + 37 38 + 37 39 + 39 42 + 39 43 + 40 42 + 41 42 + 43 44 diff --git a/src/data/amber_q/HDH.frg b/src/data/amber_q/HDH.frg new file mode 100644 index 0000000..a3a4290 --- /dev/null +++ b/src/data/amber_q/HDH.frg @@ -0,0 +1,34 @@ +# This is an automatically generated fragment file +# +$HDH + 15 1 1 0 +HDH + 1 C1 C 3 1 0 1 1 0.597879 0.000000 + 2 O1 O 0 0 0 1 1 -0.656819 0.000000 + 3 C2 CT 0 0 0 1 1 -0.065272 0.000000 + 42H2 HC 0 0 0 1 1 0.032636 0.000000 + 53H2 HC 0 0 0 1 1 0.032636 0.000000 + 6 C3 CT 0 0 0 1 1 0.378592 0.000000 + 7 H3 H1 0 0 0 1 1 -0.030998 0.000000 + 8 O3 OH 0 0 0 1 1 -0.686049 0.000000 + 9 HO3 HO 0 0 0 1 1 0.397395 0.000000 + 10 C4 CT 0 0 0 1 1 0.001626 0.000000 + 112H4 HC 0 0 0 1 1 -0.000813 0.000000 + 123H4 HC 0 0 0 1 1 -0.000813 0.000000 + 13 C5 CT 4 0 0 1 1 -0.021174 0.000000 + 142H5 HC 0 0 0 1 1 0.010587 0.000000 + 153H5 HC 0 0 0 1 1 0.010587 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 10 + 8 9 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 diff --git a/src/data/amber_q/HDH.sgm b/src/data/amber_q/HDH.sgm new file mode 100644 index 0000000..a93d547 --- /dev/null +++ b/src/data/amber_q/HDH.sgm @@ -0,0 +1,169 @@ +# This is an automatically generated segment file +# + 4.600000 + 15 14 23 30 0 0 1 1 + 0.000000 + 1 C1 3 1 0 1 1 + C 0.543709 0.000000 + 2 O1 0 0 0 1 1 + O -0.502975 0.000000 + 3 C2 0 0 0 1 1 + CT -0.180797 0.000000 + 42H2 0 0 0 1 1 + HC 0.081194 0.000000 + 53H2 0 0 0 1 1 + HC 0.081194 0.000000 + 6 C3 0 0 0 1 1 + CT -0.040127 0.000000 + 7 H3 0 0 0 1 1 + H1 0.154883 0.000000 + 8 O3 0 0 0 1 1 + OH -0.672811 0.000000 + 9 HO3 0 0 0 1 1 + HO 0.535730 0.000000 + 10 C4 0 0 0 1 1 + CT -0.100000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 13 C5 4 0 0 1 1 + CT -0.100000 0.000000 + 142H5 0 0 0 1 1 + HC 0.050000 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1 C1 C 3 1 0 1 1 0.701539 0.000000 + 2 O1 O 0 0 0 1 1 -0.605368 0.000000 + 3 C2 CT 0 0 0 1 1 0.029289 0.000000 + 42H2 HC 0 0 0 1 1 -0.027373 0.000000 + 53H2 HC 0 0 0 1 1 -0.027373 0.000000 + 6 C3 CT 0 0 0 1 1 0.003251 0.000000 + 7 H3 H1 0 0 0 1 1 0.181199 0.000000 + 8 O3 OS 4 0 0 1 1 -0.305123 0.000000 + 9 C4 CT 0 0 0 1 1 -0.239938 0.000000 + 102H4 HC 0 0 0 1 1 0.061761 0.000000 + 113H4 HC 0 0 0 1 1 0.061761 0.000000 + 12 C5 CT 5 0 0 1 1 0.202333 0.000000 + 132H5 HC 0 0 0 1 1 -0.017979 0.000000 + 143H5 HC 0 0 0 1 1 -0.017979 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 diff --git a/src/data/amber_q/HDO.sgm b/src/data/amber_q/HDO.sgm new file mode 100644 index 0000000..8b7661c --- /dev/null +++ b/src/data/amber_q/HDO.sgm @@ -0,0 +1,157 @@ +# This is an automatically generated segment file +# + 4.600000 + 14 13 22 27 0 0 1 1 + 0.000000 + 1 C1 3 1 0 1 1 + C 0.543709 0.000000 + 2 O1 0 0 0 1 1 + O -0.502975 0.000000 + 3 C2 0 0 0 1 1 + CT 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file mode 100644 index 0000000..c002678 --- /dev/null +++ b/src/data/amber_q/HED.sgm @@ -0,0 +1,161 @@ +# This is an automatically generated segment file +# + 4.600000 + 15 14 25 24 0 0 1 1 + 0.000000 + 1 NZ 0 0 0 1 1 + N3 -0.247246 0.000000 + 22HZ 0 0 0 1 1 + H 0.291236 0.000000 + 33HZ 0 0 0 1 1 + H 0.291236 0.000000 + 44HZ 0 0 0 1 1 + H 0.291236 0.000000 + 5 C1 0 0 0 1 1 + CT 0.096641 0.000000 + 62H1 0 0 0 1 1 + HP 0.073014 0.000000 + 73H1 0 0 0 1 1 + HP 0.073014 0.000000 + 8 C2 0 0 0 1 1 + CT 0.047422 0.000000 + 92H2 0 0 0 1 1 + H1 0.091922 0.000000 + 103H2 0 0 0 1 1 + H1 0.091922 0.000000 + 11 OP1 0 0 0 1 1 + OS -0.367770 0.000000 + 12 P 0 0 0 1 1 + P 0.938933 0.000000 + 13 OP2 0 0 0 1 1 + O2 -0.754754 0.000000 + 14 OP3 0 0 0 1 1 + O2 -0.754754 0.000000 + 15 OP4 3 0 0 1 1 + OS -0.367770 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 5 6 0 0 + 0.000000 0.00000E+00 + 6 5 7 0 0 + 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5 8 11 0 0 + 0 0.000000 0.00000E+00 + 19 5 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 20 9 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 21 10 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 22 8 11 12 13 0 0 + 0 0.000000 0.00000E+00 + 23 8 11 12 14 0 0 + 0 0.000000 0.00000E+00 + 24 8 11 12 15 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/HEM.frg b/src/data/amber_q/HEM.frg new file mode 100644 index 0000000..195814a --- /dev/null +++ b/src/data/amber_q/HEM.frg @@ -0,0 +1,156 @@ +$HEM + 73 1 1 0 +HEM + 1FE FE 3 0 0 1 1 1.740000 0.000000 + 2 N A NP 0 0 0 1 1 -0.840000 0.000000 + 3 C1A CC 0 4 0 1 1 0.580000 0.000000 + 4 C2A CB 0 4 0 1 1 -0.280000 0.000000 + 5 CAA CT 0 0 0 1 1 -0.100000 0.000000 + 62HAA HC 0 0 0 1 1 0.100000 0.000000 + 73HAA HC 0 0 0 1 1 0.100000 0.000000 + 8 CBA CT 0 0 0 1 1 -0.200000 0.000000 + 92HBA HC 0 0 0 1 1 0.100000 0.000000 + 103HBA HC 0 0 0 1 1 0.100000 0.000000 + 11 CGA C 0 1 0 1 1 0.350000 0.000000 + 12 O1A O2 0 0 0 1 1 -0.575000 0.000000 + 13 O2A O2 0 0 0 1 1 -0.575000 0.000000 + 14 C3A CB 0 4 0 1 1 -0.280000 0.000000 + 15 CMA CT 0 0 0 1 1 -0.150000 0.000000 + 162HMA HC 0 0 0 1 1 0.100000 0.000000 + 173HMA HC 0 0 0 1 1 0.100000 0.000000 + 184HMA HC 0 0 0 1 1 0.100000 0.000000 + 19 C4A CC 0 4 0 1 1 0.580000 0.000000 + 20 CHB CD 0 1 0 1 1 -0.640000 0.000000 + 21 HHB HC 0 0 0 1 1 0.130000 0.000000 + 22 C1B CC 0 4 0 1 1 0.580000 0.000000 + 23 N B NO 0 0 0 1 1 -0.840000 0.000000 + 24 C2B CB 0 4 0 1 1 -0.280000 0.000000 + 25 CMB CT 0 0 0 1 1 -0.150000 0.000000 + 262HMB HC 0 0 0 1 1 0.100000 0.000000 + 273HMB HC 0 0 0 1 1 0.100000 0.000000 + 284HMB HC 0 0 0 1 1 0.100000 0.000000 + 29 C3B CB 0 4 0 1 1 -0.280000 0.000000 + 30 CAB CY 0 0 0 1 1 -0.100000 0.000000 + 31 HVB HC 0 0 0 1 1 0.130000 0.000000 + 32 CBB CX 0 0 0 1 1 -0.200000 0.000000 + 332HV2 HC 0 0 0 1 1 0.100000 0.000000 + 343HV2 HC 0 0 0 1 1 0.100000 0.000000 + 35 C4B CC 0 4 0 1 1 0.580000 0.000000 + 36 CHC CD 0 1 0 1 1 -0.640000 0.000000 + 37 HHC HC 0 0 0 1 1 0.130000 0.000000 + 38 C1C CC 0 4 0 1 1 0.580000 0.000000 + 39 N C NP 0 0 0 1 1 -0.840000 0.000000 + 40 C2C CB 0 4 0 1 1 -0.280000 0.000000 + 41 CMC CT 0 0 0 1 1 -0.150000 0.000000 + 422HMC HC 0 0 0 1 1 0.100000 0.000000 + 433HMC HC 0 0 0 1 1 0.100000 0.000000 + 444HMC HC 0 0 0 1 1 0.100000 0.000000 + 45 C3C CB 0 4 0 1 1 -0.280000 0.000000 + 46 CAC CY 0 0 0 1 1 -0.100000 0.000000 + 47 HVC HC 0 0 0 1 1 0.130000 0.000000 + 48 CBC CX 0 0 0 1 1 -0.200000 0.000000 + 492HV4 HC 0 0 0 1 1 0.100000 0.000000 + 503HV4 HC 0 0 0 1 1 0.100000 0.000000 + 51 C4C CC 0 4 0 1 1 0.580000 0.000000 + 52 CHD CD 0 1 0 1 1 -0.640000 0.000000 + 53 HHD HC 0 0 0 1 1 0.130000 0.000000 + 54 C1D CC 0 4 0 1 1 0.580000 0.000000 + 55 N D NO 0 0 0 1 1 -0.840000 0.000000 + 56 C2D CB 0 4 0 1 1 -0.280000 0.000000 + 57 CMD CT 0 0 0 1 1 -0.150000 0.000000 + 582HMD HC 0 0 0 1 1 0.100000 0.000000 + 593HMD HC 0 0 0 1 1 0.100000 0.000000 + 604HMD HC 0 0 0 1 1 0.100000 0.000000 + 61 C3D CB 0 4 0 1 1 -0.280000 0.000000 + 62 C4D CC 0 4 0 1 1 0.580000 0.000000 + 63 CHA CD 0 1 0 1 1 -0.640000 0.000000 + 64 HHA HC 0 0 0 1 1 0.130000 0.000000 + 65 CAD CT 0 0 0 1 1 -0.100000 0.000000 + 662HAD HC 0 0 0 1 1 0.100000 0.000000 + 673HAD HC 0 0 0 1 1 0.100000 0.000000 + 68 CBD CT 0 0 0 1 1 -0.200000 0.000000 + 692HBD HC 0 0 0 1 1 0.100000 0.000000 + 703HBD HC 0 0 0 1 1 0.100000 0.000000 + 71 CGD C 0 1 0 1 1 0.350000 0.000000 + 72 O1D O2 0 0 0 1 1 -0.575000 0.000000 + 73 O2D O2 0 0 0 1 1 -0.575000 0.000000 + 1 2 + 1 23 + 1 39 + 1 55 + 2 3 + 2 19 + 3 4 + 3 63 + 4 5 + 4 14 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 14 15 + 14 19 + 15 16 + 15 17 + 15 18 + 19 20 + 20 21 + 20 22 + 22 23 + 22 24 + 23 35 + 24 25 + 24 29 + 25 26 + 25 27 + 25 28 + 29 30 + 29 35 + 30 31 + 30 32 + 32 33 + 32 34 + 35 36 + 36 37 + 36 38 + 38 39 + 38 40 + 39 51 + 40 41 + 40 45 + 41 42 + 41 43 + 41 44 + 45 46 + 45 51 + 46 47 + 46 48 + 48 49 + 48 50 + 51 52 + 52 53 + 52 54 + 54 55 + 54 56 + 55 62 + 56 57 + 56 61 + 57 58 + 57 59 + 57 60 + 61 62 + 61 65 + 62 63 + 63 64 + 65 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16 C6 CT 0 0 0 1 1 -0.100000 0.000000 + 172H6 HC 0 0 0 1 1 0.050000 0.000000 + 183H6 HC 0 0 0 1 1 0.050000 0.000000 + 19 C7 CT 0 0 0 1 1 -0.150000 0.000000 + 202H7 HC 0 0 0 1 1 0.050000 0.000000 + 213H7 HC 0 0 0 1 1 0.050000 0.000000 + 224H7 HC 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 + 16 17 + 16 18 + 16 19 + 19 20 + 19 21 + 19 22 diff --git a/src/data/amber_q/HEP.sgm b/src/data/amber_q/HEP.sgm new file mode 100644 index 0000000..933b1d8 --- /dev/null +++ b/src/data/amber_q/HEP.sgm @@ -0,0 +1,271 @@ +# This is an automatically generated segment file +# + 4.600000 + 22 21 39 51 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.100000 0.000000 + 22H1 0 0 0 1 1 + HC 0.050000 0.000000 + 33H1 0 0 0 1 1 + HC 0.050000 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 0 0 0 1 1 + CT -0.100000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 13 C5 0 0 0 1 1 + CT -0.100000 0.000000 + 142H5 0 0 0 1 1 + HC 0.050000 0.000000 + 153H5 0 0 0 1 1 + HC 0.050000 0.000000 + 16 C6 0 0 0 1 1 + CT -0.100000 0.000000 + 172H6 0 0 0 1 1 + HC 0.050000 0.000000 + 183H6 0 0 0 1 1 + HC 0.050000 0.000000 + 19 C7 0 0 0 1 1 + CT -0.150000 0.000000 + 202H7 0 0 0 1 1 + HC 0.050000 0.000000 + 213H7 0 0 0 1 1 + HC 0.050000 0.000000 + 224H7 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 12 10 13 0 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1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 8 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 9 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 10 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 17 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 18 4 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 19 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 20 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 21 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 22 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 24 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 25 7 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 26 7 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 27 7 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 28 11 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 29 11 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 30 11 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 31 12 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 32 12 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 33 12 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 34 10 13 16 17 0 0 + 0 0.000000 0.00000E+00 + 35 10 13 16 18 0 0 + 0 0.000000 0.00000E+00 + 36 10 13 16 19 0 0 + 0 0.000000 0.00000E+00 + 37 14 13 16 17 0 0 + 0 0.000000 0.00000E+00 + 38 14 13 16 18 0 0 + 0 0.000000 0.00000E+00 + 39 14 13 16 19 0 0 + 0 0.000000 0.00000E+00 + 40 15 13 16 17 0 0 + 0 0.000000 0.00000E+00 + 41 15 13 16 18 0 0 + 0 0.000000 0.00000E+00 + 42 15 13 16 19 0 0 + 0 0.000000 0.00000E+00 + 43 13 16 19 20 0 0 + 0 0.000000 0.00000E+00 + 44 13 16 19 21 0 0 + 0 0.000000 0.00000E+00 + 45 13 16 19 22 0 0 + 0 0.000000 0.00000E+00 + 46 17 16 19 20 0 0 + 0 0.000000 0.00000E+00 + 47 17 16 19 21 0 0 + 0 0.000000 0.00000E+00 + 48 17 16 19 22 0 0 + 0 0.000000 0.00000E+00 + 49 18 16 19 20 0 0 + 0 0.000000 0.00000E+00 + 50 18 16 19 21 0 0 + 0 0.000000 0.00000E+00 + 51 18 16 19 22 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/HP1.frg b/src/data/amber_q/HP1.frg new file mode 100644 index 0000000..40574ef --- /dev/null +++ b/src/data/amber_q/HP1.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# +$HP1 + 23 1 1 0 +HP1 + 1 C1 AC 3 0 0 1 1 -0.239301 0.000000 + 2 H1 H2 0 0 0 1 1 0.241979 0.000000 + 3 OR OS 0 0 0 1 1 -0.415373 0.000000 + 4 C2 CT 0 0 0 1 1 0.042475 0.000000 + 5 H2 H1 0 0 0 1 1 0.077985 0.000000 + 6 O2 OH 0 0 0 1 1 -0.647450 0.000000 + 7 HO2 HO 0 0 0 1 1 0.482404 0.000000 + 8 C3 CT 0 0 0 1 1 0.010480 0.000000 + 9 H3 H1 0 0 0 1 1 0.111498 0.000000 + 10 C4 CT 4 0 0 1 1 0.436393 0.000000 + 11 H4 H1 0 0 0 1 1 0.091286 0.000000 + 12 C5 CT 0 0 0 1 1 0.036980 0.000000 + 13 H5 H1 0 0 0 1 1 0.127831 0.000000 + 14 C6 CT 0 0 0 1 1 0.076400 0.000000 + 15 H6 H1 0 0 0 1 1 0.041079 0.000000 + 16 O6 OH 0 0 0 1 1 -0.406753 0.000000 + 17 HO6 HO 0 0 0 1 1 0.097859 0.000000 + 18 C7 CT 0 0 0 1 1 0.028666 0.000000 + 192H7 H1 0 0 0 1 1 0.132550 0.000000 + 203H7 H1 0 0 0 1 1 0.132550 0.000000 + 21 O7 OH 0 0 0 1 1 -0.668904 0.000000 + 22 HO7 HO 0 0 0 1 1 0.412396 0.000000 + 23 O3 OG 5 0 0 1 1 -0.203030 0.000000 + 1 2 + 1 3 + 1 4 + 3 12 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 23 + 10 11 + 10 12 + 12 13 + 12 14 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/HP2.frg b/src/data/amber_q/HP2.frg new file mode 100644 index 0000000..34e82b7 --- /dev/null +++ b/src/data/amber_q/HP2.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# +$HP2 + 22 1 1 0 +HP2 + 1 C1 AC 3 0 0 1 1 -0.010164 0.000000 + 2 H1 H2 0 0 0 1 1 0.240927 0.000000 + 3 OR OS 0 0 0 1 1 -0.252805 0.000000 + 4 C2 CT 0 0 0 1 1 -0.006072 0.000000 + 5 H2 H1 0 0 0 1 1 0.134561 0.000000 + 6 O2 OH 0 0 0 1 1 -0.610787 0.000000 + 7 HO2 HO 0 0 0 1 1 0.560263 0.000000 + 8 C3 CT 0 0 0 1 1 0.033998 0.000000 + 9 H3 H1 0 0 0 1 1 0.234578 0.000000 + 10 O3 OG 4 0 0 1 1 -0.082473 0.000000 + 11 C4 CT 5 0 0 1 1 -0.836484 0.000000 + 12 H4 H1 0 0 0 1 1 0.429570 0.000000 + 13 C5 CT 0 0 0 1 1 -0.033855 0.000000 + 14 H5 H1 0 0 0 1 1 0.246413 0.000000 + 15 C6 CT 0 0 0 1 1 0.209473 0.000000 + 16 H6 H1 0 0 0 1 1 0.201307 0.000000 + 17 O6 OH 0 0 0 1 1 -0.639374 0.000000 + 18 HO6 HO 0 0 0 1 1 0.424900 0.000000 + 19 C7 CT 0 0 0 1 1 0.105186 0.000000 + 202H7 H1 0 0 0 1 1 0.004214 0.000000 + 213H7 H1 0 0 0 1 1 0.004214 0.000000 + 22 O7 OG 6 0 0 1 1 -0.357590 0.000000 + 1 2 + 1 3 + 1 4 + 3 13 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 13 14 + 13 15 + 15 16 + 15 17 + 15 19 + 17 18 + 19 20 + 19 21 + 19 22 diff --git a/src/data/amber_q/HP3.frg b/src/data/amber_q/HP3.frg new file mode 100644 index 0000000..5325fb6 --- /dev/null +++ b/src/data/amber_q/HP3.frg @@ -0,0 +1,57 @@ +# This is an automatically generated fragment file +# +$HP3 + 26 1 1 0 +HP3 + 1 C1 AC 3 0 0 1 1 -0.181949 0.000000 + 2 H1 H2 0 0 0 1 1 0.216044 0.000000 + 3 OR OS 0 0 0 1 1 -0.229481 0.000000 + 4 C2 CT 0 0 0 1 1 0.277637 0.000000 + 5 H2 H1 0 0 0 1 1 0.089495 0.000000 + 6 O2 OH 0 0 0 1 1 -0.894528 0.000000 + 7 HO2 HO 0 0 0 1 1 0.594996 0.000000 + 8 C3 CT 0 0 0 1 1 0.029277 0.000000 + 9 H3 H1 0 0 0 1 1 0.136134 0.000000 + 10 O3 OH 0 0 0 1 1 -0.774477 0.000000 + 11 HO3 HO 0 0 0 1 1 0.501260 0.000000 + 12 C4 CT 0 0 0 1 1 0.451101 0.000000 + 13 H4 H1 0 0 0 1 1 0.070853 0.000000 + 14 O4 OH 0 0 0 1 1 -0.974205 0.000000 + 15 HO4 HO 0 0 0 1 1 0.572360 0.000000 + 16 C5 CT 0 0 0 1 1 0.055923 0.000000 + 17 H5 H1 0 0 0 1 1 0.029069 0.000000 + 18 C6 CT 0 0 0 1 1 0.244883 0.000000 + 19 H6 H1 0 0 0 1 1 0.089606 0.000000 + 20 O6 OH 0 0 0 1 1 -0.621510 0.000000 + 21 HO6 HO 0 0 0 1 1 0.412202 0.000000 + 22 C7 CT 0 0 0 1 1 0.054009 0.000000 + 232H7 H1 0 0 0 1 1 0.050176 0.000000 + 243H7 H1 0 0 0 1 1 0.050176 0.000000 + 25 O7 OH 0 0 0 1 1 -0.708732 0.000000 + 26 HO7 HO 0 0 0 1 1 0.459681 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/HP4.frg b/src/data/amber_q/HP4.frg new file mode 100644 index 0000000..03eef07 --- /dev/null +++ b/src/data/amber_q/HP4.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HP4 + 20 1 1 0 +HP4 + 1 C1 AC 0 0 0 1 1 0.000000 0.000000 + 2 O1 OG 3 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 4 0 0 1 1 -0.050000 0.000000 + 5 H2 H2 0 0 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 0 1 1 0.250000 0.000000 + 7 H3 H1 0 0 0 1 1 0.050000 0.000000 + 8 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 9 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 10 C4 CT 5 0 0 1 1 -0.050000 0.000000 + 11 H4 H1 0 0 0 1 1 0.050000 0.000000 + 12 O4 OG 6 0 0 1 1 -0.300000 0.000000 + 13 C5 CT 0 0 0 1 1 0.250000 0.000000 + 14 H5 H1 0 0 0 1 1 0.050000 0.000000 + 15 C6 CT 7 0 0 1 1 -0.050000 0.000000 + 16 H6 H1 0 0 0 1 1 0.050000 0.000000 + 17 C7 CT 0 0 0 1 1 0.200000 0.000000 + 182H7 H1 0 0 0 1 1 0.050000 0.000000 + 193H7 H1 0 0 0 1 1 0.050000 0.000000 + 20 H7 H1 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 3 13 + 4 6 + 4 7 + 6 10 + 6 11 + 6 12 + 8 9 + 8 17 + 10 13 + 10 14 + 13 15 + 13 16 + 15 17 + 15 20 + 17 18 + 17 19 diff --git a/src/data/amber_q/HP4.sgm b/src/data/amber_q/HP4.sgm new file mode 100644 index 0000000..b012eb8 --- /dev/null +++ b/src/data/amber_q/HP4.sgm @@ -0,0 +1,245 @@ +# This is an automatically generated segment file +# + 4.600000 + 20 20 35 45 0 0 1 1 + 0.000000 + 1 C1 0 0 0 1 1 + AC 0.466075 0.000000 + 2 O1 3 0 0 1 1 + OG -0.079506 0.000000 + 3 OR 0 0 0 1 1 + OS -0.455698 0.000000 + 4 C2 4 0 0 1 1 + CT -0.157271 0.000000 + 5 H2 0 0 0 1 1 + H2 -0.029617 0.000000 + 6 C3 0 0 0 1 1 + CT 0.108269 0.000000 + 7 H3 0 0 0 1 1 + H1 0.167743 0.000000 + 8 O3 0 0 0 1 1 + OH -0.608041 0.000000 + 9 HO3 0 0 0 1 1 + HO 0.393759 0.000000 + 10 C4 5 0 0 1 1 + CT -0.153131 0.000000 + 11 H4 0 0 0 1 1 + H1 0.117228 0.000000 + 12 O4 6 0 0 1 1 + OG -0.251176 0.000000 + 13 C5 0 0 0 1 1 + CT -0.415204 0.000000 + 14 H5 0 0 0 1 1 + H1 0.251985 0.000000 + 15 C6 7 0 0 1 1 + CT 0.480601 0.000000 + 16 H6 0 0 0 1 1 + H1 0.059996 0.000000 + 17 C7 0 0 0 1 1 + CT -0.114932 0.000000 + 182H7 0 0 0 1 1 + H1 0.089587 0.000000 + 193H7 0 0 0 1 1 + H1 0.089587 0.000000 + 20 H7 0 0 0 1 1 + H1 0.039746 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 3 13 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 7 0 0 + 0.000000 0.00000E+00 + 8 6 10 0 0 + 0.000000 0.00000E+00 + 9 6 11 0 0 + 0.000000 0.00000E+00 + 10 6 12 0 0 + 0.000000 0.00000E+00 + 11 8 9 0 0 + 0.000000 0.00000E+00 + 12 8 17 0 0 + 0.000000 0.00000E+00 + 13 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0.00000E+00 + 9 5 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 10 1 3 13 10 0 0 + 0 0.000000 0.00000E+00 + 11 1 3 13 15 0 0 + 0 0.000000 0.00000E+00 + 12 1 3 13 16 0 0 + 0 0.000000 0.00000E+00 + 13 1 4 6 10 0 0 + 0 0.000000 0.00000E+00 + 14 1 4 6 11 0 0 + 0 0.000000 0.00000E+00 + 15 1 4 6 12 0 0 + 0 0.000000 0.00000E+00 + 16 7 4 6 10 0 0 + 0 0.000000 0.00000E+00 + 17 7 4 6 11 0 0 + 0 0.000000 0.00000E+00 + 18 7 4 6 12 0 0 + 0 0.000000 0.00000E+00 + 19 4 6 10 13 0 0 + 0 0.000000 0.00000E+00 + 20 4 6 10 14 0 0 + 0 0.000000 0.00000E+00 + 21 11 6 10 13 0 0 + 0 0.000000 0.00000E+00 + 22 11 6 10 14 0 0 + 0 0.000000 0.00000E+00 + 23 12 6 10 13 0 0 + 0 0.000000 0.00000E+00 + 24 12 6 10 14 0 0 + 0 0.000000 0.00000E+00 + 25 9 8 17 15 0 0 + 0 0.000000 0.00000E+00 + 26 9 8 17 18 0 0 + 0 0.000000 0.00000E+00 + 27 9 8 17 19 0 0 + 0 0.000000 0.00000E+00 + 28 6 10 13 3 0 0 + 0 0.000000 0.00000E+00 + 29 6 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 30 6 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 31 14 10 13 3 0 0 + 0 0.000000 0.00000E+00 + 32 14 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 33 14 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 34 3 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 35 3 13 15 20 0 0 + 0 0.000000 0.00000E+00 + 36 10 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 37 10 13 15 20 0 0 + 0 0.000000 0.00000E+00 + 38 16 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 39 16 13 15 20 0 0 + 0 0.000000 0.00000E+00 + 40 13 15 17 8 0 0 + 0 0.000000 0.00000E+00 + 41 13 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 42 13 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 43 20 15 17 8 0 0 + 0 0.000000 0.00000E+00 + 44 20 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 45 20 15 17 19 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/HP5.frg b/src/data/amber_q/HP5.frg new file mode 100644 index 0000000..097bdfd --- /dev/null +++ b/src/data/amber_q/HP5.frg @@ -0,0 +1,65 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HP5 + 29 1 1 0 +HP5 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OG 4 0 0 1 1 -0.300000 0.000000 + 11 C4 CT 0 0 0 1 1 0.250000 0.000000 + 12 H4 H1 0 0 0 1 1 0.050000 0.000000 + 13 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 14 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 15 C5 CT 0 0 0 1 1 0.250000 0.000000 + 16 H5 H1 0 0 0 1 1 0.050000 0.000000 + 17 C6 CT 0 0 0 1 1 0.250000 0.000000 + 18 H6 H1 0 0 0 1 1 0.050000 0.000000 + 19 O6 OH 0 0 0 1 1 -0.490000 0.000000 + 20 HO6 HO 0 0 0 1 1 0.190000 0.000000 + 21 C7 CT 0 0 0 1 1 0.200000 0.000000 + 222H7 H1 0 0 0 1 1 0.050000 0.000000 + 233H7 H1 0 0 0 1 1 0.050000 0.000000 + 24 OE OS 0 0 0 1 1 -0.300000 0.000000 + 25 C8 C 0 1 0 1 1 0.640000 0.000000 + 262H8 H 0 0 0 1 1 0.270000 0.000000 + 273H8 H 0 0 0 1 1 0.270000 0.000000 + 28 O81 O 0 0 0 1 1 -0.570000 0.000000 + 29 N8 N 0 1 0 1 1 -0.610000 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 21 + 19 20 + 21 22 + 21 23 + 21 24 + 24 25 + 25 28 + 25 29 + 26 29 + 27 29 diff --git a/src/data/amber_q/HP5.sgm b/src/data/amber_q/HP5.sgm new file mode 100644 index 0000000..a7f2594 --- /dev/null +++ b/src/data/amber_q/HP5.sgm @@ -0,0 +1,373 @@ +# This is an automatically generated segment file +# + 4.600000 + 29 29 50 74 2 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC -0.013624 0.000000 + 2 H1 0 0 0 1 1 + H2 0.199162 0.000000 + 3 OR 0 0 0 1 1 + OS -0.284750 0.000000 + 4 C2 0 0 0 1 1 + CT 0.006143 0.000000 + 5 H2 0 0 0 1 1 + H1 0.212560 0.000000 + 6 O2 0 0 0 1 1 + OH -0.726817 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.495603 0.000000 + 8 C3 0 0 0 1 1 + CT 0.110882 0.000000 + 9 H3 0 0 0 1 1 + H1 0.101212 0.000000 + 10 O3 4 0 0 1 1 + OG -0.317640 0.000000 + 11 C4 0 0 0 1 1 + CT 0.272880 0.000000 + 12 H4 0 0 0 1 1 + H1 0.163223 0.000000 + 13 O4 0 0 0 1 1 + OH -0.716518 0.000000 + 14 HO4 0 0 0 1 1 + HO 0.403403 0.000000 + 15 C5 0 0 0 1 1 + CT -0.009616 0.000000 + 16 H5 0 0 0 1 1 + H1 0.157224 0.000000 + 17 C6 0 0 0 1 1 + CT 0.093350 0.000000 + 18 H6 0 0 0 1 1 + H1 0.130503 0.000000 + 19 O6 0 0 0 1 1 + OH -0.696279 0.000000 + 20 HO6 0 0 0 1 1 + HO 0.399562 0.000000 + 21 C7 0 0 0 1 1 + CT 0.028925 0.000000 + 222H7 0 0 0 1 1 + H1 0.144921 0.000000 + 233H7 0 0 0 1 1 + H1 0.144921 0.000000 + 24 OE 0 0 0 1 1 + OS -0.283339 0.000000 + 25 C8 0 1 0 1 1 + C 0.484480 0.000000 + 262H8 0 0 0 1 1 + H 0.311158 0.000000 + 273H8 0 0 0 1 1 + H 0.311158 0.000000 + 28 O81 0 0 0 1 1 + O -0.665550 0.000000 + 29 N8 0 1 0 1 1 + N -0.457137 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 15 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 8 0 0 + 0.000000 0.00000E+00 + 8 6 7 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 8 10 0 0 + 0.000000 0.00000E+00 + 11 8 11 0 0 + 0.000000 0.00000E+00 + 12 11 12 0 0 + 0.000000 0.00000E+00 + 13 11 13 0 0 + 0.000000 0.00000E+00 + 14 11 15 0 0 + 0.000000 0.00000E+00 + 15 13 14 0 0 + 0.000000 0.00000E+00 + 16 15 16 0 0 + 0.000000 0.00000E+00 + 17 15 17 0 0 + 0.000000 0.00000E+00 + 18 17 18 0 0 + 0.000000 0.00000E+00 + 19 17 19 0 0 + 0.000000 0.00000E+00 + 20 17 21 0 0 + 0.000000 0.00000E+00 + 21 19 20 0 0 + 0.000000 0.00000E+00 + 22 21 22 0 0 + 0.000000 0.00000E+00 + 23 21 23 0 0 + 0.000000 0.00000E+00 + 24 21 24 0 0 + 0.000000 0.00000E+00 + 25 24 25 0 0 + 0.000000 0.00000E+00 + 26 25 28 0 0 + 0.000000 0.00000E+00 + 27 25 29 0 0 + 0.000000 0.00000E+00 + 28 26 29 0 0 + 0.000000 0.00000E+00 + 29 27 29 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 3 15 0 0 + 0.000000 0.00000E+00 + 5 1 4 5 0 0 + 0.000000 0.00000E+00 + 6 1 4 6 0 0 + 0.000000 0.00000E+00 + 7 1 4 8 0 0 + 0.000000 0.00000E+00 + 8 5 4 6 0 0 + 0.000000 0.00000E+00 + 9 5 4 8 0 0 + 0.000000 0.00000E+00 + 10 6 4 8 0 0 + 0.000000 0.00000E+00 + 11 4 6 7 0 0 + 0.000000 0.00000E+00 + 12 4 8 9 0 0 + 0.000000 0.00000E+00 + 13 4 8 10 0 0 + 0.000000 0.00000E+00 + 14 4 8 11 0 0 + 0.000000 0.00000E+00 + 15 9 8 10 0 0 + 0.000000 0.00000E+00 + 16 9 8 11 0 0 + 0.000000 0.00000E+00 + 17 10 8 11 0 0 + 0.000000 0.00000E+00 + 18 8 11 12 0 0 + 0.000000 0.00000E+00 + 19 8 11 13 0 0 + 0.000000 0.00000E+00 + 20 8 11 15 0 0 + 0.000000 0.00000E+00 + 21 12 11 13 0 0 + 0.000000 0.00000E+00 + 22 12 11 15 0 0 + 0.000000 0.00000E+00 + 23 13 11 15 0 0 + 0.000000 0.00000E+00 + 24 11 13 14 0 0 + 0.000000 0.00000E+00 + 25 3 15 11 0 0 + 0.000000 0.00000E+00 + 26 3 15 16 0 0 + 0.000000 0.00000E+00 + 27 3 15 17 0 0 + 0.000000 0.00000E+00 + 28 11 15 16 0 0 + 0.000000 0.00000E+00 + 29 11 15 17 0 0 + 0.000000 0.00000E+00 + 30 16 15 17 0 0 + 0.000000 0.00000E+00 + 31 15 17 18 0 0 + 0.000000 0.00000E+00 + 32 15 17 19 0 0 + 0.000000 0.00000E+00 + 33 15 17 21 0 0 + 0.000000 0.00000E+00 + 34 18 17 19 0 0 + 0.000000 0.00000E+00 + 35 18 17 21 0 0 + 0.000000 0.00000E+00 + 36 19 17 21 0 0 + 0.000000 0.00000E+00 + 37 17 19 20 0 0 + 0.000000 0.00000E+00 + 38 17 21 22 0 0 + 0.000000 0.00000E+00 + 39 17 21 23 0 0 + 0.000000 0.00000E+00 + 40 17 21 24 0 0 + 0.000000 0.00000E+00 + 41 22 21 23 0 0 + 0.000000 0.00000E+00 + 42 22 21 24 0 0 + 0.000000 0.00000E+00 + 43 23 21 24 0 0 + 0.000000 0.00000E+00 + 44 21 24 25 0 0 + 0.000000 0.00000E+00 + 45 24 25 28 0 0 + 0.000000 0.00000E+00 + 46 24 25 29 0 0 + 0.000000 0.00000E+00 + 47 28 25 29 0 0 + 0.000000 0.00000E+00 + 48 25 29 26 0 0 + 0.000000 0.00000E+00 + 49 25 29 27 0 0 + 0.000000 0.00000E+00 + 50 26 29 27 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 15 0 0 + 0 0.000000 0.00000E+00 + 2 4 1 3 15 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 4 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 5 2 1 4 8 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 7 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 8 3 1 4 8 0 0 + 0 0.000000 0.00000E+00 + 9 1 3 15 11 0 0 + 0 0.000000 0.00000E+00 + 10 1 3 15 16 0 0 + 0 0.000000 0.00000E+00 + 11 1 3 15 17 0 0 + 0 0.000000 0.00000E+00 + 12 1 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 13 5 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 14 8 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 15 1 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 16 1 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 17 1 4 8 11 0 0 + 0 0.000000 0.00000E+00 + 18 5 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 19 5 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 20 5 4 8 11 0 0 + 0 0.000000 0.00000E+00 + 21 6 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 22 6 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 23 6 4 8 11 0 0 + 0 0.000000 0.00000E+00 + 24 4 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 25 4 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 26 4 8 11 15 0 0 + 0 0.000000 0.00000E+00 + 27 9 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 28 9 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 29 9 8 11 15 0 0 + 0 0.000000 0.00000E+00 + 30 10 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 31 10 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 32 10 8 11 15 0 0 + 0 0.000000 0.00000E+00 + 33 8 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 34 12 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 35 15 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 36 8 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 37 8 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 38 8 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 39 12 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 40 12 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 41 12 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 42 13 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 43 13 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 44 13 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 45 3 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 46 3 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 47 3 15 17 21 0 0 + 0 0.000000 0.00000E+00 + 48 11 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 49 11 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 50 11 15 17 21 0 0 + 0 0.000000 0.00000E+00 + 51 16 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 52 16 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 53 16 15 17 21 0 0 + 0 0.000000 0.00000E+00 + 54 15 17 19 20 0 0 + 0 0.000000 0.00000E+00 + 55 18 17 19 20 0 0 + 0 0.000000 0.00000E+00 + 56 21 17 19 20 0 0 + 0 0.000000 0.00000E+00 + 57 15 17 21 22 0 0 + 0 0.000000 0.00000E+00 + 58 15 17 21 23 0 0 + 0 0.000000 0.00000E+00 + 59 15 17 21 24 0 0 + 0 0.000000 0.00000E+00 + 60 18 17 21 22 0 0 + 0 0.000000 0.00000E+00 + 61 18 17 21 23 0 0 + 0 0.000000 0.00000E+00 + 62 18 17 21 24 0 0 + 0 0.000000 0.00000E+00 + 63 19 17 21 22 0 0 + 0 0.000000 0.00000E+00 + 64 19 17 21 23 0 0 + 0 0.000000 0.00000E+00 + 65 19 17 21 24 0 0 + 0 0.000000 0.00000E+00 + 66 17 21 24 25 0 0 + 0 0.000000 0.00000E+00 + 67 22 21 24 25 0 0 + 0 0.000000 0.00000E+00 + 68 23 21 24 25 0 0 + 0 0.000000 0.00000E+00 + 69 21 24 25 28 0 0 + 0 0.000000 0.00000E+00 + 70 21 24 25 29 0 0 + 0 0.000000 0.00000E+00 + 71 24 25 29 26 0 0 + 0 0.000000 0.00000E+00 + 72 24 25 29 27 0 0 + 0 0.000000 0.00000E+00 + 73 28 25 29 26 0 0 + 0 0.000000 0.00000E+00 + 74 28 25 29 27 0 0 + 0 0.000000 0.00000E+00 + 1 29 24 25 28 0 0 + 0 0.000000 0.00000E+00 + 2 25 26 29 27 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/HPD.frg b/src/data/amber_q/HPD.frg new file mode 100644 index 0000000..f02d0a3 --- /dev/null +++ b/src/data/amber_q/HPD.frg @@ -0,0 +1,41 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HPD + 25 1 1 0 +HPD + 1 C1 AC 0 0 0 1 1 0.270018 0.000000 + 2 H1 H2 0 0 0 1 1 0.105146 0.000000 + 3 O1 OG 3 0 0 1 1 -0.119726 0.000000 + 4 C2 CT 0 0 0 1 1 0.329208 0.000000 + 5 H2 H1 0 0 0 1 1 -0.144260 0.000000 + 6 O2 OH 0 0 0 1 1 -0.654974 0.000000 + 7 HO2 HO 0 0 0 1 1 0.335454 0.000000 + 8 C3 CT 4 0 0 1 1 0.095980 0.000000 + 9 H3 H2 0 0 0 1 1 0.004419 0.000000 + 10 C4 CT 0 0 0 1 1 0.485617 0.000000 + 11 H4 H1 0 0 0 1 1 0.046742 0.000000 + 12 O4 OH 0 0 0 1 1 -0.776649 0.000000 + 13 HO4 HO 0 0 0 1 1 0.338885 0.000000 + 14 C5 CT 0 0 0 1 1 -0.045452 0.000000 + 15 H5 H1 0 0 0 1 1 0.096821 0.000000 + 16 OR OS 0 0 0 1 1 -0.358757 0.000000 + 17 C6 CT 0 0 0 1 1 0.140161 0.000000 + 18 H6 H1 0 0 0 1 1 0.098666 0.000000 + 19 O6 OH 0 0 0 1 1 -0.699268 0.000000 + 20 HO6 HO 0 0 0 1 1 0.435355 0.000000 + 21 C7 CT 0 0 0 1 1 0.465703 0.000000 + 222H7 H1 0 0 0 1 1 -0.072464 0.000000 + 233H7 H1 0 0 0 1 1 -0.072464 0.000000 + 24 O7 OH 0 0 0 1 1 -0.748713 0.000000 + 25 HO7 HO 0 0 0 1 1 0.444552 0.000000 + 1 4 8 10 14 16 1 + 2 1 3 + 5 4 6 7 + 9 8 + 11 10 12 13 + 15 14 17 21 24 25 + 18 17 19 20 + 22 21 23 + diff --git a/src/data/amber_q/HXO.frg b/src/data/amber_q/HXO.frg new file mode 100644 index 0000000..cfa916f --- /dev/null +++ b/src/data/amber_q/HXO.frg @@ -0,0 +1,38 @@ +# This is an automatically generated fragment file +# +$HXO + 17 1 1 0 +HXO + 1 C1 C 3 1 0 1 1 0.576548 0.000000 + 2 O1 O2 0 0 0 1 1 -0.716030 0.000000 + 3 C2 CT 0 0 0 1 1 0.150222 0.000000 + 42H2 HC 0 0 0 1 1 -0.005370 0.000000 + 53H2 HC 0 0 0 1 1 -0.005370 0.000000 + 6 C3 CT 0 0 0 1 1 0.002475 0.000000 + 72H3 HC 0 0 0 1 1 -0.001237 0.000000 + 83H3 HC 0 0 0 1 1 -0.001237 0.000000 + 9 C4 CT 0 0 0 1 1 0.014959 0.000000 + 102H4 HC 0 0 0 1 1 -0.007480 0.000000 + 113H4 HC 0 0 0 1 1 -0.007480 0.000000 + 12 C5 CT 0 0 0 1 1 0.032564 0.000000 + 132H5 HC 0 0 0 1 1 -0.016282 0.000000 + 143H5 HC 0 0 0 1 1 -0.016282 0.000000 + 15 C6 CT 4 0 0 1 1 0.090772 0.000000 + 162H6 HC 0 0 0 1 1 -0.045386 0.000000 + 173H6 HC 0 0 0 1 1 -0.045386 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 12 15 + 15 16 + 15 17 diff --git a/src/data/amber_q/IPS.frg b/src/data/amber_q/IPS.frg new file mode 100644 index 0000000..aa7ed7a --- /dev/null +++ b/src/data/amber_q/IPS.frg @@ -0,0 +1,16 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$IPS + 5 1 1 0 +IPS + 1 P P 0 0 0 1 1 0.000000 0.000000 + 2 O1 O2 0 0 0 1 1 -0.500000 0.000000 + 3 O2 O2 0 0 0 1 1 -0.500000 0.000000 + 4 O3 O2 0 0 0 1 1 -0.500000 0.000000 + 5 O4 O2 0 0 0 1 1 -0.500000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/KD1.frg b/src/data/amber_q/KD1.frg new file mode 100644 index 0000000..9eabeb9 --- /dev/null +++ b/src/data/amber_q/KD1.frg @@ -0,0 +1,57 @@ +# This is an automatically generated fragment file +# +$KD1 + 26 1 1 0 +KD1 + 1 C1 C 0 1 0 1 1 0.518979 0.000000 + 2 O1 O 0 0 0 1 1 -0.508304 0.000000 + 3 O OH 0 0 0 1 1 -0.279281 0.000000 + 4 HO HO 0 0 0 1 1 0.360363 0.000000 + 5 OR OS 0 0 0 1 1 -0.294817 0.000000 + 6 C2 AC 3 0 0 1 1 0.036168 0.000000 + 7 C3 CT 0 0 0 1 1 -0.154673 0.000000 + 82H3 HC 0 0 0 1 1 0.125934 0.000000 + 93H3 HC 0 0 0 1 1 0.125934 0.000000 + 10 C4 CT 0 0 0 1 1 -0.065200 0.000000 + 11 H4 H1 0 0 0 1 1 0.193700 0.000000 + 12 C5 CT 0 0 0 1 1 0.020912 0.000000 + 13 H5 H1 0 0 0 1 1 0.171043 0.000000 + 14 C6 CT 0 0 0 1 1 -0.006439 0.000000 + 15 H6 H1 0 0 0 1 1 0.128707 0.000000 + 16 C7 CT 0 0 0 1 1 0.204488 0.000000 + 17 H7 H1 0 0 0 1 1 0.150785 0.000000 + 18 O7 OH 0 0 0 1 1 -0.696350 0.000000 + 19 HO7 HO 0 0 0 1 1 0.472670 0.000000 + 20 C8 CT 0 0 0 1 1 0.006360 0.000000 + 212H8 H1 0 0 0 1 1 0.092572 0.000000 + 223H8 H1 0 0 0 1 1 0.092572 0.000000 + 23 O8 OH 0 0 0 1 1 -0.659409 0.000000 + 24 HO8 HO 0 0 0 1 1 0.385334 0.000000 + 25 O4 OG 4 0 0 1 1 -0.267058 0.000000 + 26 O5 OG 5 0 0 1 1 -0.154990 0.000000 + 1 2 + 1 3 + 1 6 + 3 4 + 5 6 + 5 14 + 6 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 25 + 12 13 + 12 14 + 12 26 + 14 15 + 14 16 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 23 + 23 24 diff --git a/src/data/amber_q/KD2.frg b/src/data/amber_q/KD2.frg new file mode 100644 index 0000000..ef58053 --- /dev/null +++ b/src/data/amber_q/KD2.frg @@ -0,0 +1,59 @@ +# This is an automatically generated fragment file +# +$KD2 + 27 1 1 0 +KD2 + 1 C1 C 0 1 0 1 1 0.547862 0.000000 + 2 O1 O 0 0 0 1 1 -0.540830 0.000000 + 3 O OH 0 0 0 1 1 -0.269611 0.000000 + 4 HO HO 0 0 0 1 1 0.336841 0.000000 + 5 OR OS 0 0 0 1 1 -0.338267 0.000000 + 6 C2 CT 3 0 0 1 1 0.224276 0.000000 + 7 C3 CT 0 0 0 1 1 -0.099141 0.000000 + 82H3 HC 0 0 0 1 1 0.092366 0.000000 + 93H3 HC 0 0 0 1 1 0.092366 0.000000 + 10 C4 CT 0 0 0 1 1 -0.010965 0.000000 + 11 H4 H1 0 0 0 1 1 0.109685 0.000000 + 12 C5 CT 0 0 0 1 1 0.055712 0.000000 + 13 H5 H1 0 0 0 1 1 -0.152967 0.000000 + 14 O5 OH 0 0 0 1 1 -0.463618 0.000000 + 15 HO5 HO 0 0 0 1 1 0.366899 0.000000 + 16 C6 CT 0 0 0 1 1 -0.055565 0.000000 + 17 H6 H1 0 0 0 1 1 0.278002 0.000000 + 18 C7 CT 0 0 0 1 1 0.091959 0.000000 + 19 H7 H1 0 0 0 1 1 0.178914 0.000000 + 20 O7 OH 0 0 0 1 1 -1.022990 0.000000 + 21 HO7 HO 0 0 0 1 1 0.766683 0.000000 + 22 C8 CT 0 0 0 1 1 0.048311 0.000000 + 232H8 H1 0 0 0 1 1 0.029467 0.000000 + 243H8 H1 0 0 0 1 1 0.029467 0.000000 + 25 O8 OH 0 0 0 1 1 -0.413185 0.000000 + 26 HO8 HO 0 0 0 1 1 0.337109 0.000000 + 27 O4 OG 4 0 0 1 1 -0.218780 0.000000 + 1 2 + 1 3 + 1 6 + 3 4 + 5 6 + 5 16 + 6 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 27 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/KD3.frg b/src/data/amber_q/KD3.frg new file mode 100644 index 0000000..782a3c6 --- /dev/null +++ b/src/data/amber_q/KD3.frg @@ -0,0 +1,59 @@ +# This is an automatically generated fragment file +# +$KD3 + 27 1 1 0 +KD3 + 1 C1 C 0 1 0 1 1 1.044383 0.000000 + 2 O1A O2 0 0 0 1 1 -0.935696 0.000000 + 3 O1B O2 0 0 0 1 1 -0.935696 0.000000 + 4 OR OS 0 0 0 1 1 -0.169597 0.000000 + 5 C2 AC 3 0 0 1 1 0.172224 0.000000 + 6 C3 CT 0 0 0 1 1 -0.256355 0.000000 + 72H3 HC 0 0 0 1 1 0.125604 0.000000 + 83H3 HC 0 0 0 1 1 0.125604 0.000000 + 9 C4 CT 0 0 0 1 1 0.121398 0.000000 + 10 H4 H1 0 0 0 1 1 0.084283 0.000000 + 11 O4 OH 0 0 0 1 1 -0.642891 0.000000 + 12 HO4 HO 0 0 0 1 1 0.436456 0.000000 + 13 C5 CT 0 0 0 1 1 0.091253 0.000000 + 14 H5 H1 0 0 0 1 1 -0.134499 0.000000 + 15 O5 OH 0 0 0 1 1 -0.594336 0.000000 + 16 HO5 HO 0 0 0 1 1 0.472890 0.000000 + 17 C6 CT 0 0 0 1 1 -0.183187 0.000000 + 18 H6 H1 0 0 0 1 1 0.123957 0.000000 + 19 C7 CT 0 0 0 1 1 0.086963 0.000000 + 20 H7 H1 0 0 0 1 1 0.184972 0.000000 + 21 O7 OH 0 0 0 1 1 -0.332596 0.000000 + 22 HO7 HO 0 0 0 1 1 0.099128 0.000000 + 23 C8 CT 0 0 0 1 1 0.141777 0.000000 + 242H8 H1 0 0 0 1 1 0.052594 0.000000 + 253H8 H1 0 0 0 1 1 0.052594 0.000000 + 26 O8 OH 0 0 0 1 1 -0.603639 0.000000 + 27 HO8 HO 0 0 0 1 1 0.372412 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 17 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 13 + 11 12 + 13 14 + 13 15 + 13 17 + 15 16 + 17 18 + 17 19 + 19 20 + 19 21 + 19 23 + 21 22 + 23 24 + 23 25 + 23 26 + 26 27 diff --git a/src/data/amber_q/KD4.frg b/src/data/amber_q/KD4.frg new file mode 100644 index 0000000..55afd7d --- /dev/null +++ b/src/data/amber_q/KD4.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$KD4 + 24 1 1 0 +KD4 + 1 C1 C 0 1 0 1 1 0.800000 0.000000 + 2 O1 O2 0 0 0 1 1 -0.900000 0.000000 + 3 O O2 0 0 0 1 1 -0.900000 0.000000 + 4 OR OS 0 0 0 1 1 -0.300000 0.000000 + 5 C2 AC 3 0 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 0 1 1 -0.100000 0.000000 + 72H3 HC 0 0 0 1 1 0.050000 0.000000 + 83H3 HC 0 0 0 1 1 0.050000 0.000000 + 9 C4 CT 0 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 0 1 1 0.050000 0.000000 + 11 O4 OG 4 0 0 1 1 -0.300000 0.000000 + 12 C5 CT 5 0 0 1 1 -0.050000 0.000000 + 13 H5 H1 0 0 0 1 1 0.050000 0.000000 + 14 C6 CT 0 0 0 1 1 0.250000 0.000000 + 15 H6 H1 0 0 0 1 1 0.050000 0.000000 + 16 C7 CT 0 0 0 1 1 0.250000 0.000000 + 17 H7 H1 0 0 0 1 1 0.050000 0.000000 + 18 O7 OH 0 0 0 1 1 -0.490000 0.000000 + 19 HO7 HO 0 0 0 1 1 0.190000 0.000000 + 20 C8 CT 0 0 0 1 1 0.200000 0.000000 + 212H8 H1 0 0 0 1 1 0.050000 0.000000 + 223H8 H1 0 0 0 1 1 0.050000 0.000000 + 23 O8 OH 0 0 0 1 1 -0.490000 0.000000 + 24 HO8 HO 0 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 14 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 23 + 23 24 diff --git a/src/data/amber_q/KD4.sgm b/src/data/amber_q/KD4.sgm new file mode 100644 index 0000000..ea87111 --- /dev/null +++ b/src/data/amber_q/KD4.sgm @@ -0,0 +1,307 @@ +# This is an automatically generated segment file +# + 4.600000 + 24 24 42 60 1 0 1 1 + 0.000000 + 1 C1 0 1 0 1 1 + C 0.473407 0.000000 + 2 O1 0 0 0 1 1 + O2 -0.736704 0.000000 + 3 O 0 0 0 1 1 + O2 -0.736704 0.000000 + 4 OR 0 0 0 1 1 + OS -0.605275 0.000000 + 5 C2 3 0 0 1 1 + AC 0.339543 0.000000 + 6 C3 0 0 0 1 1 + CT -0.018770 0.000000 + 72H3 0 0 0 1 1 + HC 0.108290 0.000000 + 83H3 0 0 0 1 1 + HC 0.108290 0.000000 + 9 C4 0 0 0 1 1 + CT 0.015472 0.000000 + 10 H4 0 0 0 1 1 + H1 0.171605 0.000000 + 11 O4 4 0 0 1 1 + OG -0.263850 0.000000 + 12 C5 5 0 0 1 1 + CT -0.362258 0.000000 + 13 H5 0 0 0 1 1 + H1 0.255752 0.000000 + 14 C6 0 0 0 1 1 + CT -0.133148 0.000000 + 15 H6 0 0 0 1 1 + H1 0.128242 0.000000 + 16 C7 0 0 0 1 1 + CT 0.603049 0.000000 + 17 H7 0 0 0 1 1 + H1 0.023453 0.000000 + 18 O7 0 0 0 1 1 + OH -0.728146 0.000000 + 19 HO7 0 0 0 1 1 + HO 0.466143 0.000000 + 20 C8 0 0 0 1 1 + CT 0.001132 0.000000 + 212H8 0 0 0 1 1 + H1 0.100000 0.000000 + 223H8 0 0 0 1 1 + H1 0.100000 0.000000 + 23 O8 0 0 0 1 1 + OH -0.728146 0.000000 + 24 HO8 0 0 0 1 1 + HO 0.418623 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 5 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 14 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 6 7 0 0 + 0.000000 0.00000E+00 + 8 6 8 0 0 + 0.000000 0.00000E+00 + 9 6 9 0 0 + 0.000000 0.00000E+00 + 10 9 10 0 0 + 0.000000 0.00000E+00 + 11 9 11 0 0 + 0.000000 0.00000E+00 + 12 9 12 0 0 + 0.000000 0.00000E+00 + 13 12 13 0 0 + 0.000000 0.00000E+00 + 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0.00000E+00 + 45 15 14 16 20 0 0 + 0 0.000000 0.00000E+00 + 46 14 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 47 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 48 20 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 49 14 16 20 21 0 0 + 0 0.000000 0.00000E+00 + 50 14 16 20 22 0 0 + 0 0.000000 0.00000E+00 + 51 14 16 20 23 0 0 + 0 0.000000 0.00000E+00 + 52 17 16 20 21 0 0 + 0 0.000000 0.00000E+00 + 53 17 16 20 22 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 20 23 0 0 + 0 0.000000 0.00000E+00 + 55 18 16 20 21 0 0 + 0 0.000000 0.00000E+00 + 56 18 16 20 22 0 0 + 0 0.000000 0.00000E+00 + 57 18 16 20 23 0 0 + 0 0.000000 0.00000E+00 + 58 16 20 23 24 0 0 + 0 0.000000 0.00000E+00 + 59 21 20 23 24 0 0 + 0 0.000000 0.00000E+00 + 60 22 20 23 24 0 0 + 0 0.000000 0.00000E+00 + 1 5 3 1 2 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/KD5.frg b/src/data/amber_q/KD5.frg new file mode 100644 index 0000000..5e2171b --- /dev/null +++ b/src/data/amber_q/KD5.frg @@ -0,0 +1,61 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$KD5 + 27 1 1 0 +KD5 + 1 C1 C 0 1 0 1 1 0.800000 0.000000 + 2 O1 O2 0 0 0 1 1 -0.900000 0.000000 + 3 O O2 0 0 0 1 1 -0.900000 0.000000 + 4 OR OS 0 0 0 1 1 -0.300000 0.000000 + 5 C2 AC 3 0 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 0 1 1 -0.100000 0.000000 + 72H3 HC 0 0 0 1 1 0.050000 0.000000 + 83H3 HC 0 0 0 1 1 0.050000 0.000000 + 9 C4 CT 0 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 0 1 1 0.050000 0.000000 + 11 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 12 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 13 C5 CT 0 0 0 1 1 0.250000 0.000000 + 14 H5 H1 0 0 0 1 1 0.050000 0.000000 + 15 O5 OH 0 0 0 1 1 -0.490000 0.000000 + 16 HO5 HO 0 0 0 1 1 0.190000 0.000000 + 17 C6 CT 0 0 0 1 1 0.250000 0.000000 + 18 H6 H1 0 0 0 1 1 0.050000 0.000000 + 19 C7 CT 0 0 0 1 1 0.250000 0.000000 + 20 H7 H1 0 0 0 1 1 0.050000 0.000000 + 21 O7 OH 0 0 0 1 1 -0.490000 0.000000 + 22 HO7 HO 0 0 0 1 1 0.190000 0.000000 + 23 C8 CT 0 0 0 1 1 0.200000 0.000000 + 242H8 H1 0 0 0 1 1 0.050000 0.000000 + 253H8 H1 0 0 0 1 1 0.050000 0.000000 + 26 O8 OH 0 0 0 1 1 -0.490000 0.000000 + 27 HO8 HO 0 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 17 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 13 + 11 12 + 13 14 + 13 15 + 13 17 + 15 16 + 17 18 + 17 19 + 19 20 + 19 21 + 19 23 + 21 22 + 23 24 + 23 25 + 23 26 + 26 27 diff --git a/src/data/amber_q/KD5.sgm b/src/data/amber_q/KD5.sgm new file mode 100644 index 0000000..64fb001 --- /dev/null +++ b/src/data/amber_q/KD5.sgm @@ -0,0 +1,353 @@ +# This is an automatically generated segment file +# + 4.600000 + 27 27 47 72 1 0 1 1 + 0.000000 + 1 C1 0 1 0 1 1 + C 0.473407 0.000000 + 2 O1 0 0 0 1 1 + O2 -0.736704 0.000000 + 3 O 0 0 0 1 1 + O2 -0.736704 0.000000 + 4 OR 0 0 0 1 1 + OS -0.605275 0.000000 + 5 C2 3 0 0 1 1 + AC 0.339543 0.000000 + 6 C3 0 0 0 1 1 + CT -0.018770 0.000000 + 72H3 0 0 0 1 1 + HC 0.078388 0.000000 + 83H3 0 0 0 1 1 + HC 0.078388 0.000000 + 9 C4 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--- /dev/null +++ b/src/data/amber_q/KDN.frg @@ -0,0 +1,43 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$KDN + 26 1 1 0 +KDN + 1 C1 C 0 1 0 1 1 1.257694 0.000000 + 2 O1 O2 0 0 0 1 1 -1.011582 0.000000 + 3 O O2 0 0 0 1 1 -1.011582 0.000000 + 4 C2 AC 3 0 0 1 1 0.200039 0.000000 + 5 C3 CT 0 0 0 1 1 0.076646 0.000000 + 62H3 HC 0 0 0 1 1 -0.120006 0.000000 + 73H3 HC 0 0 0 1 1 -0.120006 0.000000 + 8 C4 CT 0 0 0 1 1 0.808356 0.000000 + 9 H4 H1 0 0 0 1 1 -0.081409 0.000000 + 10 O4 OH 0 0 0 1 1 -0.777757 0.000000 + 11 HO4 HO 0 0 0 1 1 0.327976 0.000000 + 12 C5 CT 5 0 0 1 1 -0.487865 0.000000 + 13 H5 H1 0 0 0 1 1 0.138770 0.000000 + 14 C6 CT 0 0 0 1 1 0.448428 0.000000 + 15 H6 H1 0 0 0 1 1 -0.088631 0.000000 + 16 OR OS 0 0 0 1 1 -0.653128 0.000000 + 17 C7 CT 0 0 0 1 1 0.387545 0.000000 + 18 H7 H1 0 0 0 1 1 -0.084796 0.000000 + 19 O7 OH 0 0 0 1 1 -0.757907 0.000000 + 20 HO7 HO 0 0 0 1 1 0.419274 0.000000 + 21 C8 CT 0 0 0 1 1 0.632846 0.000000 + 222H8 H1 0 0 0 1 1 -0.071639 0.000000 + 233H8 H1 0 0 0 1 1 -0.071639 0.000000 + 24 N8 N 0 0 0 1 1 -1.228155 0.000000 + 252HN8 H 0 0 0 1 1 0.434264 0.000000 + 263HN8 H 0 0 0 1 1 0.434264 0.000000 + 1 4 5 8 12 14 16 4 + 2 1 3 + 6 5 7 + 9 8 10 11 + 12 13 + 15 14 17 21 24 + 18 17 19 20 + 22 21 23 + 25 24 26 + diff --git a/src/data/amber_q/LCX.frg b/src/data/amber_q/LCX.frg new file mode 100644 index 0000000..6ce5774 --- /dev/null +++ b/src/data/amber_q/LCX.frg @@ -0,0 +1,61 @@ +# Charges from 6-31G* optimized B3LYP/DZVP structure +# Using single-stage RESP fit +# +# esp +# range 0.4; spacing 0.035; factor 1.0 +# constrain xhn 2 5 4 3 +# constrain xhn 10 13 12 11 +# constrain 0.7341 9 +# constrain -0.5894 14 +# constrain -0.3479 1 +# constrain 0.2747 6 +# constrain equal 30 31 +# +$LCX + 23 1 1 0 +LCX + 1 N N 1 1 0 1 1 -0.347900 0.000000 + 2 H2 H 0 0 0 1 1 0.274700 0.000000 + 3 CA CT 0 0 0 1 1 -0.498102 0.000000 + 4 HA H1 0 0 0 1 1 0.082916 0.000000 + 5 C C 2 1 0 1 1 0.734100 0.000000 + 6 O O 0 0 0 1 1 -0.589400 0.000000 + 7 CB CT 0 0 0 1 1 0.707723 0.000000 + 82HB HC 0 0 0 1 1 -0.197502 0.000000 + 93HB HC 0 0 0 1 1 -0.115759 0.000000 + 10 CG CT 0 0 0 1 1 -0.029147 0.000000 + 112HG HC 0 0 0 1 1 0.002345 0.000000 + 123HG HC 0 0 0 1 1 -0.058389 0.000000 + 13 CD CT 0 0 0 1 1 -0.142735 0.000000 + 142HD HC 0 0 0 1 1 -0.039196 0.000000 + 153HD HC 0 0 0 1 1 0.062913 0.000000 + 16 CE CT 0 0 0 1 1 0.727637 0.000000 + 172HE H1 0 0 0 1 1 -0.139613 0.000000 + 183HE H1 0 0 0 1 1 -0.165745 0.000000 + 19 NZ NT 0 0 0 1 1 -0.921043 0.000000 + 202HZ H 0 0 0 1 1 0.305925 0.000000 + 21 CX C 0 1 0 1 1 1.074896 0.000000 + 22 OX1 O2 0 0 0 1 1 -0.864312 0.000000 + 23 OX2 O2 0 0 0 1 1 -0.864312 0.000000 + 1 3 + 1 2 + 3 7 + 3 5 + 3 4 + 5 6 + 7 10 + 7 9 + 7 8 + 10 13 + 10 12 + 10 11 + 13 16 + 13 15 + 13 14 + 16 19 + 16 18 + 16 17 + 19 21 + 19 20 + 21 23 + 21 22 diff --git a/src/data/amber_q/LPO.sgm b/src/data/amber_q/LPO.sgm new file mode 100644 index 0000000..dd6b06a --- /dev/null +++ b/src/data/amber_q/LPO.sgm @@ -0,0 +1,177 @@ +# This is an automatically generated segment file +# + 4.600000 + 17 16 24 28 1 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT 0.135769 0.000000 + 22H1 0 0 0 1 1 + H1 0.053943 0.000000 + 33H1 0 0 0 1 1 + H1 0.053943 0.000000 + 4 C2 0 0 0 1 1 + CT 0.196572 0.000000 + 5 H2 0 0 0 1 1 + H1 -0.018013 0.000000 + 6 O2 0 0 0 1 1 + OS -0.536934 0.000000 + 7 C3 0 0 0 1 1 + CT 0.298340 0.000000 + 82H3 0 0 0 1 1 + H1 0.007352 0.000000 + 93H3 0 0 0 1 1 + H1 0.007352 0.000000 + 10 O3 0 0 0 1 1 + OS -0.536934 0.000000 + 11 C4 4 1 0 1 1 + C 0.834997 0.000000 + 12 O4 0 0 0 1 1 + O -0.557784 0.000000 + 13 C5 0 1 0 1 1 + C 0.834997 0.000000 + 14 O5 0 0 0 1 1 + O -0.557784 0.000000 + 15 C6 5 0 0 1 1 + CT -0.083934 0.000000 + 162H6 0 0 0 1 1 + HC 0.036918 0.000000 + 173H6 0 0 0 1 1 + HC 0.036918 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 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0 0 + 0 0.000000 0.00000E+00 + 16 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 17 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 18 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 19 4 6 13 14 0 0 + 0 0.000000 0.00000E+00 + 20 4 6 13 15 0 0 + 0 0.000000 0.00000E+00 + 21 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 22 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 24 7 10 11 12 0 0 + 0 0.000000 0.00000E+00 + 25 6 13 15 16 0 0 + 0 0.000000 0.00000E+00 + 26 6 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 27 14 13 15 16 0 0 + 0 0.000000 0.00000E+00 + 28 14 13 15 17 0 0 + 0 0.000000 0.00000E+00 + 1 15 6 13 14 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/MA2.sgm b/src/data/amber_q/MA2.sgm new file mode 100644 index 0000000..cc2145f --- /dev/null +++ b/src/data/amber_q/MA2.sgm @@ -0,0 +1,401 @@ +# This is an automatically generated segment file +# + 4.600000 + 31 31 55 76 5 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + EC -0.369000 40.000000 + 2 H1 0 0 0 1 1 + H2 0.215830 20.000000 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29 0 0 + 0 0.000000 0.00000E+00 + 46 15 14 25 26 0 0 + 0 0.000000 0.00000E+00 + 47 15 14 25 27 0 0 + 0 0.000000 0.00000E+00 + 48 15 14 25 29 0 0 + 0 0.000000 0.00000E+00 + 49 16 14 25 26 0 0 + 0 0.000000 0.00000E+00 + 50 16 14 25 27 0 0 + 0 0.000000 0.00000E+00 + 51 16 14 25 29 0 0 + 0 0.000000 0.00000E+00 + 52 14 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 53 14 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 56 16 18 19 20 0 0 + 0 0.000000 0.00000E+00 + 57 21 18 19 20 0 0 + 0 0.000000 0.00000E+00 + 58 16 18 21 22 0 0 + 0 0.000000 0.00000E+00 + 59 16 18 21 23 0 0 + 0 0.000000 0.00000E+00 + 60 16 18 21 24 0 0 + 0 0.000000 0.00000E+00 + 61 19 18 21 22 0 0 + 0 0.000000 0.00000E+00 + 62 19 18 21 23 0 0 + 0 0.000000 0.00000E+00 + 63 19 18 21 24 0 0 + 0 0.000000 0.00000E+00 + 64 14 25 27 28 0 0 + 0 0.000000 0.00000E+00 + 65 26 25 27 28 0 0 + 0 0.000000 0.00000E+00 + 66 29 25 27 28 0 0 + 0 0.000000 0.00000E+00 + 67 14 25 29 3 0 0 + 0 0.000000 0.00000E+00 + 68 14 25 29 30 0 0 + 0 0.000000 0.00000E+00 + 69 14 25 29 31 0 0 + 0 0.000000 0.00000E+00 + 70 26 25 29 3 0 0 + 0 0.000000 0.00000E+00 + 71 26 25 29 30 0 0 + 0 0.000000 0.00000E+00 + 72 26 25 29 31 0 0 + 0 0.000000 0.00000E+00 + 73 27 25 29 3 0 0 + 0 0.000000 0.00000E+00 + 74 27 25 29 30 0 0 + 0 0.000000 0.00000E+00 + 75 27 25 29 31 0 0 + 0 0.000000 0.00000E+00 + 76 3 29 31 32 0 0 + 0 0.000000 0.00000E+00 + 77 3 29 31 33 0 0 + 0 0.000000 0.00000E+00 + 78 25 29 31 32 0 0 + 0 0.000000 0.00000E+00 + 79 25 29 31 33 0 0 + 0 0.000000 0.00000E+00 + 80 30 29 31 32 0 0 + 0 0.000000 0.00000E+00 + 81 30 29 31 33 0 0 + 0 0.000000 0.00000E+00 + 1 4 8 6 7 0 0 + 0 0.000000 0.00000E+00 + 2 10 6 8 9 0 0 + 0 0.000000 0.00000E+00 + 3 14 18 16 17 0 0 + 0 0.000000 0.00000E+00 + 4 21 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 5 29 32 31 33 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/MAN.frg b/src/data/amber_q/MAN.frg new file mode 100644 index 0000000..7ff1222 --- /dev/null +++ b/src/data/amber_q/MAN.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$MAN + 20 1 1 0 +MAN + 1 C1 AC 3 0 0 1 1 -0.162607 0.000000 + 2 H1 H2 0 0 0 1 1 0.182851 0.000000 + 3 C2 CT 0 0 0 1 1 -0.080535 0.000000 + 4 H2 H1 0 0 0 1 1 0.173175 0.000000 + 5 O2 OG 4 0 0 1 1 -0.079068 0.000000 + 6 C3 CT 0 0 0 1 1 0.020952 0.000000 + 7 H3 H1 0 0 0 1 1 0.156462 0.000000 + 8 C4 CT 0 0 0 1 1 0.277312 0.000000 + 9 H4 H1 0 0 0 1 1 0.055141 0.000000 + 10 O4 OH 0 0 0 1 1 -0.666790 0.000000 + 11 HO4 HO 0 0 0 1 1 0.440190 0.000000 + 12 C5 CT 0 0 0 1 1 -0.000761 0.000000 + 13 H5 H1 0 0 0 1 1 0.105583 0.000000 + 14 OR OS 0 0 0 1 1 -0.246681 0.000000 + 15 C6 CT 0 0 0 1 1 0.090569 0.000000 + 162H6 H1 0 0 0 1 1 0.071777 0.000000 + 173H6 H1 0 0 0 1 1 0.071777 0.000000 + 18 O6 OH 0 0 0 1 1 -0.573637 0.000000 + 19 HO6 HO 0 0 0 1 1 0.359359 0.000000 + 20 O3 OG 5 0 0 1 1 -0.195069 0.000000 + 1 2 + 1 3 + 1 14 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 20 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 15 + 15 16 + 15 17 + 15 18 + 18 19 diff --git a/src/data/amber_q/NH4.frg b/src/data/amber_q/NH4.frg new file mode 100644 index 0000000..c14a6c7 --- /dev/null +++ b/src/data/amber_q/NH4.frg @@ -0,0 +1,16 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$NH4 + 5 1 1 0 +NH4 + 1 N N 0 0 0 1 1 -0.200000 0.000000 + 22H H 0 0 0 1 1 0.300000 0.000000 + 33H H 0 0 0 1 1 0.300000 0.000000 + 44H H 0 0 0 1 1 0.300000 0.000000 + 55H H 0 0 0 1 1 0.300000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/NTR.frg b/src/data/amber_q/NTR.frg new file mode 100644 index 0000000..2f28f4a --- /dev/null +++ b/src/data/amber_q/NTR.frg @@ -0,0 +1,13 @@ +# N-terminal cap fragment +# +$NTR + 6 1 1 0 +NTR + 1 C1 CT 0 0 0 1 1 -0.150000 0.000000 + 22H1 HC 0 0 0 1 1 0.050000 0.000000 + 33H1 HC 0 0 0 1 1 0.050000 0.000000 + 44H1 HC 0 0 0 1 1 0.050000 0.000000 + 5 C C 3 0 0 1 1 0.597300 0.000000 + 6 O O 0 0 0 1 1 -0.597300 0.000000 + 2 1 5 6 + 3 1 4 diff --git a/src/data/amber_q/Na.sgm b/src/data/amber_q/Na.sgm new file mode 100644 index 0000000..6698860 --- /dev/null +++ b/src/data/amber_q/Na.sgm @@ -0,0 +1,7 @@ +# This is an automatically generated segment file +# + 4.600000 + 1 0 0 0 0 0 1 1 + 0.000000 + 1Na 0 0 0 1 1 + Na 1.000000 0.000000 diff --git a/src/data/amber_q/O4P.frg b/src/data/amber_q/O4P.frg new file mode 100644 index 0000000..0e5096c --- /dev/null +++ b/src/data/amber_q/O4P.frg @@ -0,0 +1,14 @@ +# This is an automatically generated fragment file +# +$O4P + 5 1 1 0 +O4P + 1 P P 3 0 0 1 1 1.222551 0.000000 + 2 OP1 OS 4 0 0 1 1 -0.275749 0.000000 + 3 OP2 O2 0 0 0 1 1 -0.818353 0.000000 + 4 OP3 O2 0 0 0 1 1 -0.818353 0.000000 + 5 OP4 OS 5 0 0 1 1 -0.310096 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/PET.frg b/src/data/amber_q/PET.frg new file mode 100644 index 0000000..32fef1d --- /dev/null +++ b/src/data/amber_q/PET.frg @@ -0,0 +1,38 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$PET + 16 1 1 0 +PET + 1 C1 CT 3 0 0 1 1 -0.100000 0.000000 + 22H1 HC 0 0 0 1 1 0.050000 0.000000 + 33H1 HC 0 0 0 1 1 0.050000 0.000000 + 4 C2 CT 0 0 0 1 1 -0.100000 0.000000 + 52H2 HC 0 0 0 1 1 0.050000 0.000000 + 63H2 HC 0 0 0 1 1 0.050000 0.000000 + 7 C3 CT 0 0 0 1 1 -0.100000 0.000000 + 82H3 HC 0 0 0 1 1 0.050000 0.000000 + 93H3 HC 0 0 0 1 1 0.050000 0.000000 + 10 C4 CT 0 0 0 1 1 -0.100000 0.000000 + 112H4 HC 0 0 0 1 1 0.050000 0.000000 + 123H4 HC 0 0 0 1 1 0.050000 0.000000 + 13 C5 CT 0 0 0 1 1 -0.150000 0.000000 + 142H5 HC 0 0 0 1 1 0.050000 0.000000 + 153H5 HC 0 0 0 1 1 0.050000 0.000000 + 164H5 HC 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 diff --git a/src/data/amber_q/PET.sgm b/src/data/amber_q/PET.sgm new file mode 100644 index 0000000..5f5d6cb --- /dev/null +++ b/src/data/amber_q/PET.sgm @@ -0,0 +1,187 @@ +# This is an automatically generated segment file +# + 4.600000 + 16 15 27 33 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.026814 0.000000 + 22H1 0 0 0 1 1 + HC 0.013407 0.000000 + 33H1 0 0 0 1 1 + HC 0.013407 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 0 0 0 1 1 + CT -0.100000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 13 C5 0 0 0 1 1 + CT -0.150000 0.000000 + 142H5 0 0 0 1 1 + HC 0.050000 0.000000 + 153H5 0 0 0 1 1 + HC 0.050000 0.000000 + 164H5 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 12 10 13 0 0 + 0.000000 0.00000E+00 + 13 13 14 0 0 + 0.000000 0.00000E+00 + 14 13 15 0 0 + 0.000000 0.00000E+00 + 15 13 16 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 4 5 0 0 + 0.000000 0.00000E+00 + 5 1 4 6 0 0 + 0.000000 0.00000E+00 + 6 1 4 7 0 0 + 0.000000 0.00000E+00 + 7 5 4 6 0 0 + 0.000000 0.00000E+00 + 8 5 4 7 0 0 + 0.000000 0.00000E+00 + 9 6 4 7 0 0 + 0.000000 0.00000E+00 + 10 4 7 8 0 0 + 0.000000 0.00000E+00 + 11 4 7 9 0 0 + 0.000000 0.00000E+00 + 12 4 7 10 0 0 + 0.000000 0.00000E+00 + 13 8 7 9 0 0 + 0.000000 0.00000E+00 + 14 8 7 10 0 0 + 0.000000 0.00000E+00 + 15 9 7 10 0 0 + 0.000000 0.00000E+00 + 16 7 10 11 0 0 + 0.000000 0.00000E+00 + 17 7 10 12 0 0 + 0.000000 0.00000E+00 + 18 7 10 13 0 0 + 0.000000 0.00000E+00 + 19 11 10 12 0 0 + 0.000000 0.00000E+00 + 20 11 10 13 0 0 + 0.000000 0.00000E+00 + 21 12 10 13 0 0 + 0.000000 0.00000E+00 + 22 10 13 14 0 0 + 0.000000 0.00000E+00 + 23 10 13 15 0 0 + 0.000000 0.00000E+00 + 24 10 13 16 0 0 + 0.000000 0.00000E+00 + 25 14 13 15 0 0 + 0.000000 0.00000E+00 + 26 14 13 16 0 0 + 0.000000 0.00000E+00 + 27 15 13 16 0 0 + 0.000000 0.00000E+00 + 1 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 8 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 9 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 10 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 17 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 18 4 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 19 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 20 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 21 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 22 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 24 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 25 7 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 26 7 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 27 7 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 28 11 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 29 11 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 30 11 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 31 12 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 32 12 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 33 12 10 13 16 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/PNT.frg b/src/data/amber_q/PNT.frg new file mode 100644 index 0000000..685a3c9 --- /dev/null +++ b/src/data/amber_q/PNT.frg @@ -0,0 +1,34 @@ +# This is an automatically generated fragment file +# +$PNT + 15 1 1 0 +PNT + 1 C1 CT 3 0 0 1 1 0.033906 0.000000 + 22H1 HC 0 0 0 1 1 -0.016953 0.000000 + 33H1 HC 0 0 0 1 1 -0.016953 0.000000 + 4 C2 CT 0 0 0 1 1 0.004668 0.000000 + 52H2 HC 0 0 0 1 1 -0.002334 0.000000 + 63H2 HC 0 0 0 1 1 -0.002334 0.000000 + 7 C3 CT 0 0 0 1 1 0.013981 0.000000 + 82H3 HC 0 0 0 1 1 -0.006990 0.000000 + 93H3 HC 0 0 0 1 1 -0.006990 0.000000 + 10 C4 CT 0 0 0 1 1 0.012201 0.000000 + 112H4 HC 0 0 0 1 1 -0.006101 0.000000 + 123H4 HC 0 0 0 1 1 -0.006101 0.000000 + 13 C5 CT 4 0 0 1 1 0.017278 0.000000 + 142H5 HC 0 0 0 1 1 -0.008639 0.000000 + 153H5 HC 0 0 0 1 1 -0.008639 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 diff --git a/src/data/amber_q/PO4.frg b/src/data/amber_q/PO4.frg new file mode 100644 index 0000000..619f3e1 --- /dev/null +++ b/src/data/amber_q/PO4.frg @@ -0,0 +1,14 @@ +# This is an automatically generated fragment file +# +$PO4 + 5 1 1 0 +PO4 + 1 OP1 OS 3 0 0 1 1 -0.139474 0.000000 + 2 P P 0 0 0 1 1 0.938933 0.000000 + 3 OP2 O2 0 0 0 1 1 -0.933153 0.000000 + 4 OP3 O2 0 0 0 1 1 -0.933153 0.000000 + 5 OP4 O2 0 0 0 1 1 -0.933153 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 diff --git a/src/data/amber_q/PO4.sgm b/src/data/amber_q/PO4.sgm new file mode 100644 index 0000000..0436063 --- /dev/null +++ b/src/data/amber_q/PO4.sgm @@ -0,0 +1,35 @@ +# This is an automatically generated segment file +# + 4.600000 + 5 4 6 0 0 0 1 1 + 0.000000 + 1 OP1 3 0 0 1 1 + OS -0.139474 0.000000 + 2 P 0 0 0 1 1 + P 0.938933 0.000000 + 3 OP2 0 0 0 1 1 + O2 -0.933153 0.000000 + 4 OP3 0 0 0 1 1 + O2 -0.933153 0.000000 + 5 OP4 0 0 0 1 1 + O2 -0.933153 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 2 3 0 0 + 0.000000 0.00000E+00 + 3 2 4 0 0 + 0.000000 0.00000E+00 + 4 2 5 0 0 + 0.000000 0.00000E+00 + 1 1 2 3 0 0 + 0.000000 0.00000E+00 + 2 1 2 4 0 0 + 0.000000 0.00000E+00 + 3 1 2 5 0 0 + 0.000000 0.00000E+00 + 4 3 2 4 0 0 + 0.000000 0.00000E+00 + 5 3 2 5 0 0 + 0.000000 0.00000E+00 + 6 4 2 5 0 0 + 0.000000 0.00000E+00 diff --git a/src/data/amber_q/PPO.frg b/src/data/amber_q/PPO.frg new file mode 100644 index 0000000..c7fa76d --- /dev/null +++ b/src/data/amber_q/PPO.frg @@ -0,0 +1,22 @@ +# This is an automatically generated fragment file +# +$PPO + 9 1 1 0 +PPO + 1 O11 OS 3 0 0 1 1 -0.429501 0.000000 + 2 P1 P 0 0 0 1 1 0.311885 0.000000 + 3 O12 O2 0 0 0 1 1 -0.490521 0.000000 + 4 O13 O2 0 0 0 1 1 -0.490521 0.000000 + 5 O14 OS 0 0 0 1 1 -0.118311 0.000000 + 6 P2 P 0 0 0 1 1 1.139199 0.000000 + 7 O21 O2 0 0 0 1 1 -0.755746 0.000000 + 8 O22 O2 0 0 0 1 1 -0.755746 0.000000 + 9 O23 OS 4 0 0 1 1 -0.410738 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 + 5 6 + 6 7 + 6 8 + 6 9 diff --git a/src/data/amber_q/RH2.frg b/src/data/amber_q/RH2.frg new file mode 100644 index 0000000..6d7ce2c --- /dev/null +++ b/src/data/amber_q/RH2.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$RH2 + 20 1 1 0 +RH2 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OG 4 0 0 1 1 -0.300000 0.000000 + 7 C3 CT 0 0 0 1 1 0.250000 0.000000 + 8 H3 H1 0 0 0 1 1 0.050000 0.000000 + 9 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 10 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 11 C4 CT 0 0 0 1 1 0.250000 0.000000 + 12 H4 H1 0 0 0 1 1 0.050000 0.000000 + 13 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 14 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 15 C5 CT 0 0 0 1 1 0.250000 0.000000 + 16 H5 H1 0 0 0 1 1 0.050000 0.000000 + 17 C6 CT 0 0 0 1 1 -0.150000 0.000000 + 182H6 HC 0 0 0 1 1 0.050000 0.000000 + 193H6 HC 0 0 0 1 1 0.050000 0.000000 + 204H6 HC 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/RH2.sgm b/src/data/amber_q/RH2.sgm new file mode 100644 index 0000000..7b6754c --- /dev/null +++ b/src/data/amber_q/RH2.sgm @@ -0,0 +1,263 @@ +# This is an automatically generated segment file +# + 4.600000 + 20 20 36 53 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC -0.207395 0.000000 + 2 H1 0 0 0 1 1 + H2 0.118124 0.000000 + 3 OR 0 0 0 1 1 + OS -0.192617 0.000000 + 4 C2 0 0 0 1 1 + CT -0.071635 0.000000 + 5 H2 0 0 0 1 1 + H1 0.157937 0.000000 + 6 O2 4 0 0 1 1 + OG -0.052212 0.000000 + 7 C3 0 0 0 1 1 + CT 0.232988 0.000000 + 8 H3 0 0 0 1 1 + H1 0.167022 0.000000 + 9 O3 0 0 0 1 1 + OH -0.680086 0.000000 + 10 HO3 0 0 0 1 1 + HO 0.402264 0.000000 + 11 C4 0 0 0 1 1 + CT 0.192216 0.000000 + 12 H4 0 0 0 1 1 + H1 0.062758 0.000000 + 13 O4 0 0 0 1 1 + OH -0.690913 0.000000 + 14 HO4 0 0 0 1 1 + HO 0.418323 0.000000 + 15 C5 0 0 0 1 1 + CT 0.087070 0.000000 + 16 H5 0 0 0 1 1 + H1 0.088853 0.000000 + 17 C6 0 0 0 1 1 + CT -0.261219 0.000000 + 182H6 0 0 0 1 1 + HC 0.076174 0.000000 + 193H6 0 0 0 1 1 + HC 0.076174 0.000000 + 204H6 0 0 0 1 1 + HC 0.076174 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 15 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 7 0 0 + 0.000000 0.00000E+00 + 8 7 8 0 0 + 0.000000 0.00000E+00 + 9 7 9 0 0 + 0.000000 0.00000E+00 + 10 7 11 0 0 + 0.000000 0.00000E+00 + 11 9 10 0 0 + 0.000000 0.00000E+00 + 12 11 12 0 0 + 0.000000 0.00000E+00 + 13 11 13 0 0 + 0.000000 0.00000E+00 + 14 11 15 0 0 + 0.000000 0.00000E+00 + 15 13 14 0 0 + 0.000000 0.00000E+00 + 16 15 16 0 0 + 0.000000 0.00000E+00 + 17 15 17 0 0 + 0.000000 0.00000E+00 + 18 17 18 0 0 + 0.000000 0.00000E+00 + 19 17 19 0 0 + 0.000000 0.00000E+00 + 20 17 20 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 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17 0 0 + 0.000000 0.00000E+00 + 30 16 15 17 0 0 + 0.000000 0.00000E+00 + 31 15 17 18 0 0 + 0.000000 0.00000E+00 + 32 15 17 19 0 0 + 0.000000 0.00000E+00 + 33 15 17 20 0 0 + 0.000000 0.00000E+00 + 34 18 17 19 0 0 + 0.000000 0.00000E+00 + 35 18 17 20 0 0 + 0.000000 0.00000E+00 + 36 19 17 20 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 15 0 0 + 0 0.000000 0.00000E+00 + 2 4 1 3 15 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 4 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 5 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 7 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 8 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 9 1 3 15 11 0 0 + 0 0.000000 0.00000E+00 + 10 1 3 15 16 0 0 + 0 0.000000 0.00000E+00 + 11 1 3 15 17 0 0 + 0 0.000000 0.00000E+00 + 12 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 13 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 14 1 4 7 11 0 0 + 0 0.000000 0.00000E+00 + 15 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 16 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 17 5 4 7 11 0 0 + 0 0.000000 0.00000E+00 + 18 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 19 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 20 6 4 7 11 0 0 + 0 0.000000 0.00000E+00 + 21 4 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 22 8 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 23 11 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 24 4 7 11 12 0 0 + 0 0.000000 0.00000E+00 + 25 4 7 11 13 0 0 + 0 0.000000 0.00000E+00 + 26 4 7 11 15 0 0 + 0 0.000000 0.00000E+00 + 27 8 7 11 12 0 0 + 0 0.000000 0.00000E+00 + 28 8 7 11 13 0 0 + 0 0.000000 0.00000E+00 + 29 8 7 11 15 0 0 + 0 0.000000 0.00000E+00 + 30 9 7 11 12 0 0 + 0 0.000000 0.00000E+00 + 31 9 7 11 13 0 0 + 0 0.000000 0.00000E+00 + 32 9 7 11 15 0 0 + 0 0.000000 0.00000E+00 + 33 7 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 34 12 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 35 15 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 36 7 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 37 7 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 38 7 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 39 12 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 40 12 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 41 12 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 42 13 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 43 13 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 44 13 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 45 3 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 46 3 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 47 3 15 17 20 0 0 + 0 0.000000 0.00000E+00 + 48 11 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 49 11 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 50 11 15 17 20 0 0 + 0 0.000000 0.00000E+00 + 51 16 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 52 16 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 53 16 15 17 20 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/RH3.sgm b/src/data/amber_q/RH3.sgm new file mode 100644 index 0000000..188a645 --- /dev/null +++ b/src/data/amber_q/RH3.sgm @@ -0,0 +1,263 @@ +# This is an automatically generated segment file +# + 4.600000 + 20 20 36 53 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC -0.369034 0.000000 + 2 H1 0 0 0 1 1 + H2 0.361771 0.000000 + 3 OR 0 0 0 1 1 + OS -0.196302 0.000000 + 4 C2 0 0 0 1 1 + CT -0.037888 0.000000 + 5 H2 0 0 0 1 1 + H1 0.040713 0.000000 + 6 O2 0 0 0 1 1 + OH -0.513798 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.499911 0.000000 + 8 C3 0 0 0 1 1 + CT 0.050318 0.000000 + 9 H3 0 0 0 1 1 + H1 0.141515 0.000000 + 10 O3 4 0 0 1 1 + OG -0.186064 0.000000 + 11 C4 0 0 0 1 1 + CT 0.242973 0.000000 + 12 H4 0 0 0 1 1 + H1 0.131167 0.000000 + 13 O4 0 0 0 1 1 + OH -0.633238 0.000000 + 14 HO4 0 0 0 1 1 + HO 0.376917 0.000000 + 15 C5 0 0 0 1 1 + CT 0.007763 0.000000 + 16 H5 0 0 0 1 1 + H1 0.083275 0.000000 + 17 C6 0 0 0 1 1 + CT -0.119723 0.000000 + 182H6 0 0 0 1 1 + HC 0.039908 0.000000 + 193H6 0 0 0 1 1 + HC 0.039908 0.000000 + 204H6 0 0 0 1 1 + HC 0.039908 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 15 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 8 0 0 + 0.000000 0.00000E+00 + 8 6 7 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 8 10 0 0 + 0.000000 0.00000E+00 + 11 8 11 0 0 + 0.000000 0.00000E+00 + 12 11 12 0 0 + 0.000000 0.00000E+00 + 13 11 13 0 0 + 0.000000 0.00000E+00 + 14 11 15 0 0 + 0.000000 0.00000E+00 + 15 13 14 0 0 + 0.000000 0.00000E+00 + 16 15 16 0 0 + 0.000000 0.00000E+00 + 17 15 17 0 0 + 0.000000 0.00000E+00 + 18 17 18 0 0 + 0.000000 0.00000E+00 + 19 17 19 0 0 + 0.000000 0.00000E+00 + 20 17 20 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 3 15 0 0 + 0.000000 0.00000E+00 + 5 1 4 5 0 0 + 0.000000 0.00000E+00 + 6 1 4 6 0 0 + 0.000000 0.00000E+00 + 7 1 4 8 0 0 + 0.000000 0.00000E+00 + 8 5 4 6 0 0 + 0.000000 0.00000E+00 + 9 5 4 8 0 0 + 0.000000 0.00000E+00 + 10 6 4 8 0 0 + 0.000000 0.00000E+00 + 11 4 6 7 0 0 + 0.000000 0.00000E+00 + 12 4 8 9 0 0 + 0.000000 0.00000E+00 + 13 4 8 10 0 0 + 0.000000 0.00000E+00 + 14 4 8 11 0 0 + 0.000000 0.00000E+00 + 15 9 8 10 0 0 + 0.000000 0.00000E+00 + 16 9 8 11 0 0 + 0.000000 0.00000E+00 + 17 10 8 11 0 0 + 0.000000 0.00000E+00 + 18 8 11 12 0 0 + 0.000000 0.00000E+00 + 19 8 11 13 0 0 + 0.000000 0.00000E+00 + 20 8 11 15 0 0 + 0.000000 0.00000E+00 + 21 12 11 13 0 0 + 0.000000 0.00000E+00 + 22 12 11 15 0 0 + 0.000000 0.00000E+00 + 23 13 11 15 0 0 + 0.000000 0.00000E+00 + 24 11 13 14 0 0 + 0.000000 0.00000E+00 + 25 3 15 11 0 0 + 0.000000 0.00000E+00 + 26 3 15 16 0 0 + 0.000000 0.00000E+00 + 27 3 15 17 0 0 + 0.000000 0.00000E+00 + 28 11 15 16 0 0 + 0.000000 0.00000E+00 + 29 11 15 17 0 0 + 0.000000 0.00000E+00 + 30 16 15 17 0 0 + 0.000000 0.00000E+00 + 31 15 17 18 0 0 + 0.000000 0.00000E+00 + 32 15 17 19 0 0 + 0.000000 0.00000E+00 + 33 15 17 20 0 0 + 0.000000 0.00000E+00 + 34 18 17 19 0 0 + 0.000000 0.00000E+00 + 35 18 17 20 0 0 + 0.000000 0.00000E+00 + 36 19 17 20 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 15 0 0 + 0 0.000000 0.00000E+00 + 2 4 1 3 15 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 4 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 5 2 1 4 8 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 7 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 8 3 1 4 8 0 0 + 0 0.000000 0.00000E+00 + 9 1 3 15 11 0 0 + 0 0.000000 0.00000E+00 + 10 1 3 15 16 0 0 + 0 0.000000 0.00000E+00 + 11 1 3 15 17 0 0 + 0 0.000000 0.00000E+00 + 12 1 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 13 5 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 14 8 4 6 7 0 0 + 0 0.000000 0.00000E+00 + 15 1 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 16 1 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 17 1 4 8 11 0 0 + 0 0.000000 0.00000E+00 + 18 5 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 19 5 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 20 5 4 8 11 0 0 + 0 0.000000 0.00000E+00 + 21 6 4 8 9 0 0 + 0 0.000000 0.00000E+00 + 22 6 4 8 10 0 0 + 0 0.000000 0.00000E+00 + 23 6 4 8 11 0 0 + 0 0.000000 0.00000E+00 + 24 4 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 25 4 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 26 4 8 11 15 0 0 + 0 0.000000 0.00000E+00 + 27 9 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 28 9 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 29 9 8 11 15 0 0 + 0 0.000000 0.00000E+00 + 30 10 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 31 10 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 32 10 8 11 15 0 0 + 0 0.000000 0.00000E+00 + 33 8 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 34 12 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 35 15 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 36 8 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 37 8 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 38 8 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 39 12 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 40 12 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 41 12 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 42 13 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 43 13 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 44 13 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 45 3 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 46 3 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 47 3 15 17 20 0 0 + 0 0.000000 0.00000E+00 + 48 11 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 49 11 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 50 11 15 17 20 0 0 + 0 0.000000 0.00000E+00 + 51 16 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 52 16 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 53 16 15 17 20 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/RHA.frg b/src/data/amber_q/RHA.frg new file mode 100644 index 0000000..78d85c6 --- /dev/null +++ b/src/data/amber_q/RHA.frg @@ -0,0 +1,45 @@ +# This is an automatically generated fragment file +# +$RHA + 20 1 1 0 +RHA + 1 C1 AC 3 0 0 1 1 -0.362918 0.000000 + 2 H1 H2 0 0 0 1 1 0.338065 0.000000 + 3 C2 CT 0 0 0 1 1 0.081671 0.000000 + 4 H2 H1 0 0 0 1 1 0.117337 0.000000 + 5 O2 OH 0 0 0 1 1 -0.580083 0.000000 + 6 HO2 HO 0 0 0 1 1 0.420095 0.000000 + 7 C3 CT 0 0 0 1 1 0.055135 0.000000 + 8 H3 H1 0 0 0 1 1 0.089139 0.000000 + 9 O3 OH 0 0 0 1 1 -0.613470 0.000000 + 10 HO3 HO 0 0 0 1 1 0.429006 0.000000 + 11 C4 CT 0 0 0 1 1 0.090177 0.000000 + 12 H4 H1 0 0 0 1 1 0.199352 0.000000 + 13 O4 OG 4 0 0 1 1 -0.206307 0.000000 + 14 C5 CT 0 0 0 1 1 0.091230 0.000000 + 15 H5 H1 0 0 0 1 1 0.074855 0.000000 + 16 OR OS 0 0 0 1 1 -0.233814 0.000000 + 17 C6 CT 0 0 0 1 1 -0.204654 0.000000 + 182H6 HC 0 0 0 1 1 0.071728 0.000000 + 193H6 HC 0 0 0 1 1 0.071728 0.000000 + 204H6 HC 0 0 0 1 1 0.071728 0.000000 + 1 2 + 1 3 + 1 16 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/SEP.frg b/src/data/amber_q/SEP.frg new file mode 100644 index 0000000..9ea24ce --- /dev/null +++ b/src/data/amber_q/SEP.frg @@ -0,0 +1,30 @@ +$SEP + 14 1 1 0 +SEP + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.824145 0.000000 + 4 HA H1 0 0 0 1 1 0.402169 0.000000 + 5 CB CT 0 0 0 1 1 1.255182 0.000000 + 62HB H1 0 0 0 1 1 -0.181987 0.000000 + 73HB H1 0 0 0 1 1 -0.252644 0.000000 + 8 OG OS 0 0 0 1 1 -0.906468 0.000000 + 9 C C 2 1 0 1 1 0.597300 0.000000 + 10 O O 0 0 0 1 1 -0.567900 0.000000 + 11 P P 0 0 0 1 1 1.848480 0.000000 + 12 O1P O2 0 0 0 1 1 -1.082268 0.000000 + 13 O2P O2 0 0 0 1 1 -1.078626 0.000000 + 14 O3P O2 0 0 0 1 1 -1.065292 0.000000 + 1 2 + 1 3 + 3 9 + 3 4 + 3 5 + 5 8 + 5 6 + 5 7 + 8 11 + 9 10 + 11 14 + 11 12 + 11 13 diff --git a/src/data/amber_q/SO4.frg b/src/data/amber_q/SO4.frg new file mode 100644 index 0000000..b2ddb1d --- /dev/null +++ b/src/data/amber_q/SO4.frg @@ -0,0 +1,16 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$SO4 + 5 1 1 0 +SO4 + 1 S S 0 0 0 1 1 0.000000 0.000000 + 2 O1 O2 0 0 0 1 1 -0.500000 0.000000 + 3 O2 O2 0 0 0 1 1 -0.500000 0.000000 + 4 O3 O2 0 0 0 1 1 -0.500000 0.000000 + 5 O4 O2 0 0 0 1 1 -0.500000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/TPO.frg b/src/data/amber_q/TPO.frg new file mode 100644 index 0000000..36a6c07 --- /dev/null +++ b/src/data/amber_q/TPO.frg @@ -0,0 +1,41 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude estimates +# 11/08/04 18:38:58 +# +$TPO + 17 1 1 0 +TPO + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.639337 0.000000 + 4 HA H1 0 0 0 1 1 0.123871 0.000000 + 5 CB CT 0 0 0 1 1 1.565340 0.000000 + 6 HB H1 0 0 0 1 1 -0.209754 0.000000 + 7 CG2 CT 0 0 0 1 1 -0.680243 0.000000 + 82HG2 HC 0 0 0 1 1 0.057615 0.000000 + 93HG2 HC 0 0 0 1 1 0.044406 0.000000 + 104HG2 HC 0 0 0 1 1 0.137305 0.000000 + 11 OG1 OS 0 0 0 1 1 -0.897338 0.000000 + 12 C C 2 1 0 1 1 0.597300 0.000000 + 13 O O 0 0 0 1 1 -0.567900 0.000000 + 14 O3 O2 0 0 0 1 1 -1.112264 0.000000 + 15 O2 O2 0 0 0 1 1 -1.025128 0.000000 + 16 O1 O2 0 0 0 1 1 -1.089571 0.000000 + 17 P P 0 0 0 1 1 1.839497 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 12 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 17 + 12 13 + 14 17 + 15 17 + 16 17 diff --git a/src/data/amber_q/amber.par b/src/data/amber_q/amber.par new file mode 100644 index 0000000..1c1f802 --- /dev/null +++ b/src/data/amber_q/amber.par @@ -0,0 +1,219 @@ +This is the AMBER96 user defined parameter file for NWChem 3.2 and ARGOS 7.0 +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +Ne 20.17900 3.16779E-01 1.55006E-01 1 1111111111 + 10 1.58389E-01 1.55006E-01 TPS000106 JCP 85, 6720-6727 (1986) +Mg 24.30500 4.30952E-02 1.36000E-01 1 1111111111 + 12 2.15476E-02 1.36000E-01 TPS000106 JCC 12, 1125-1128 (1991) +Ca 40.08000 3.78520E-02 1.74000E-01 1 1111111111 + 20 1.89260E-02 1.74000E-01 TPS000106 JCC 12, 1125-1128 (1991) +Sr 87.62000 2.70286E-01 1.92000E-01 1 1111111111 + 38 1.35143E-01 1.92000E-01 TPS000106 JCC 12, 1125-1128 (1991) +Cl 35.45300 4.44950E-01 2.50000E-01 1 1111111111 + 17 2.22475E-01 2.50000E-01 +CD 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +CY 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +CX 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +NO 14.00674 7.11283E-01 1.82400E-01 1 1111111111 + 7 3.55641E-01 1.82400E-01 +NP 14.00674 7.11283E-01 1.82400E-01 1 1111111111 + 7 3.55641E-01 1.82400E-01 +Cross +Bonds +FE -NO 0.20100 4.18400E+04 +FE -NP 0.20100 4.18400E+04 +CC -NP 0.13840 2.64429E+05 +CB -CC 0.14440 2.28446E+05 +CC -CD 0.13910 3.27189E+05 +CB -CT 0.15010 2.48530E+05 +HC -CD 0.10900 2.82838E+05 +CC -NO 0.13840 2.64429E+05 +CB -CY 0.15010 2.48530E+05 +HC -CY 0.10900 2.84512E+05 +CX -CY 0.13400 4.76976E+05 +HC -CX 0.10900 2.84512E+05 +AC -H2 0.10900 2.84512E+05 tps990729 copy CT-H2 +EC -H2 0.10900 2.84512E+05 tps990729 copy CT-H2 +C -OS 0.14100 2.67776E+05 tps990729 copy CT-OS +C -AC 0.15220 2.65266E+05 tps990729 copy C-CT +S -O2 0.14900 1.69566E+05 tps991219 for SO4-- taken from Smith +Angles +C -CT -OH 1.91114 4.18400E+02 +CB -CB -CC 1.86750 5.85760E+02 +CB -CB -CT 2.23751 5.85760E+02 +CB -CB -CY 2.23751 5.85760E+02 +CB -CC -CD 2.18864 5.85760E+02 +CB -CC -NO 1.92510 5.85760E+02 +CB -CC -NP 1.92510 5.85760E+02 +CD -CC -NO 2.19039 5.85760E+02 +CD -CC -NP 2.19039 5.85760E+02 +CC -CB -CT 2.17992 5.85760E+02 +CC -CB -CY 2.17992 5.85760E+02 +HC -CD -CC 2.05949 2.51040E+02 +CC -CD -CC 2.16595 5.85760E+02 +HC -CT -CB 1.91114 2.92880E+02 +CB -CT -CT 1.98968 5.27184E+02 +CT -CT -Cl 1.91986 3.55810E+02 +Cl -CT -Cl 1.94604 4.18600E+02 +HC -CX -HC 2.09440 2.92880E+02 +HC -CX -CY 2.09440 2.92880E+02 +HC -CY -CB 2.09440 2.92880E+02 +HC -CY -CX 2.09440 2.92880E+02 +CB -CY -CX 2.09440 5.85760E+02 +CC -NO -CC 1.83958 5.85760E+02 +CC -NO -FE 2.22355 2.51040E+02 +CC -NP -CC 1.83958 5.85760E+02 +CC -NP -FE 2.22355 2.51040E+02 +NB -FE -NO 1.57080 4.18400E+02 +NB -FE -NP 1.57080 4.18400E+02 +NO -FE -NO 1.57080 0.00000E+00 +NO -FE -NP 1.57080 4.18400E+02 +NP -FE -NP 1.57080 0.00000E+00 +N2 -CA -CT 2.09440 5.85760E+02 rdl000731 taken from N2-CA-N2 +CM -C -O2 2.04204 5.85760E+02 tps020326 taken from CT-C-O2 +CB -CT -S 2.00189 4.18400E+02 tps020326 taken from CT-CT-S +CB -CT -H1 1.91114 4.18400E+02 tps020326 taken from CM-CT-H1 +H2 -AC -OS 1.91114 4.18400E+02 tps990729 copy H2-CT-OS +H2 -AC -OG 1.91114 4.18400E+02 tps990729 copy H2-CT-OS +H2 -EC -OG 1.91114 4.18400E+02 tps000315 copy H2-CT-OS +H2 -EC -OS 1.91114 4.18400E+02 tps980817 +OS -AC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-OS +OS -EC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-H2 +CT -AC -H2 1.91114 4.18400E+02 tps980817 +CT -EC -H2 1.91114 4.18400E+02 tps980817 +AC -CT -H1 1.91114 4.18400E+02 tps990729 copy CT-CT-H1 +EC -CT -H1 1.91114 4.18400E+02 tps980817 +AC -CT -N 1.91114 4.18400E+02 tps990729 copy CT-CT-N* +EC -CT -N 1.91114 4.18400E+02 tps980817 +CT -OS -C 1.91114 5.02080E+02 tps990729 copy CT-OS-CT +H1 -CT -OG 1.91114 4.18400E+02 tps990729 copy H1-CT-OS +CT -OG -CT 1.91114 5.02080E+02 tps990729 copy CT-OS-CT +AC -OS -P 2.10312 8.36800E+02 tps980817 copy CT-OS-P +EC -OS -P 2.10312 8.36800E+02 tps980817 +OS -C -O 2.19911 6.69440E+02 tps980817 +CT -C -OS 2.04204 5.85760E+02 tps980817 +AC -C -O 2.10138 6.69440E+02 tps990729 copy CT-C-O +AC -C -OH 2.04204 5.85760E+02 tps990729 copy CT-C-OH +C -AC -OG 1.91114 4.18400E+02 tps990729 copy CT-CT-OS +C -AC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-OS +C -AC -CT 1.93906 5.27184E+02 tps990729 copy C-CT-CT +OG -CT -C 1.91114 4.18400E+02 tps990729 copy OS-CT-CT +OS -CT -C 1.91114 4.18400E+02 tps990729 copy OS-CT-CT +OG -CT -OS 1.91114 4.18400E+02 tps990729 copy N*-CT-OS +AC -C -O2 2.04204 5.85760E+02 tps990729 copy CT-C-O2 +OS -C -O2 2.19911 6.69440E+02 tps990729 copy O2-C-O2 +Proper dihedrals + -NB -FE - 0.00000 0.00000E+02 2 + -NO -FE - 3.14159 0.00000E+02 2 + -NP -FE - 3.14159 0.00000E+02 2 + -CB -CC - 3.14159 3.29490E+00 2 + -CB -CT - 3.14159 0.00000E+00 2 + -CB -CY - 3.14159 0.00000E+00 2 + -CC -CD - 3.14159 8.26340E+00 2 + -CC -NO - 3.14159 5.96220E+00 2 + -CC -NP - 3.14159 5.96220E+00 2 + -CX -CY - 3.14159 3.13800E+01 2 + -C -OS - 3.14159 6.06680E+00 2 tps990729 copy -C-N*- + -AC -OG - 0.00000 1.60387E+00 3 tps990729 copy -CT-OS- + -EC -OG - 0.00000 1.60387E+00 3 tps000315 copy -CT-OS- +C -AC -OG -CT 0.52360 1.58992E+00 -3 tps990729 copy CT-CT-OS-CT +C -AC -OG -CT 3.14159 4.18400E-01 2 tps990729 copy CT-CT-OS-CT + -C -AC - 0.00000 0.00000E+00 2 tps990729 copy -C-CT- +CT -EC -N -H 0.00000 0.00000E+00 1 +CT -EC -OH -HO 0.00000 6.97333E-01 3 +Improper dihedrals + - -CC -CC 3.14159 4.18400E+00 2 + - -CC -CB 3.14159 4.18400E+00 2 + - -CB -NP 3.14159 4.18400E+00 2 + - -CB -NO 3.14159 4.18400E+00 2 + - -CB -CY 3.14159 4.18400E+00 2 + - -CB -CT 3.14159 4.18400E+00 2 + - -CD -HC 3.14159 4.18400E+00 2 + - -N* -H 3.14159 4.50240E+00 2 +Atom types +Li 3 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Na 11 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Mg 12 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +K 19 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Ca 20 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Rb 37 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Sr 38 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Cl 17 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +O2 8 0 0 0 1 15 4 808 1808 800 + 0 0 0 0 0 + 0 0 0 0 0 +# +O2 8 0 0 0 1 15 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N 7 0 0 0 3 1 0 0 0 0 + 15 4 0 0 0 + 15 4 0 0 0 +# +N3 7 0 0 0 3 6 4 0 0 0 + 6 4 0 0 0 + 6 4 0 0 0 +O2 8 0 0 0 1 16 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +S 16 0 0 0 4 8 0 0 0 0 + 8 0 0 0 0 + 8 0 0 0 0 +NB 7 0 0 0 3 1 0 0 0 0 + 6 3 7 1 0 + 6 3 6 6 0 +# +CB 6 0 0 66 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N3 7 0 0 0 4 6 0 0 0 0 + 6 0 0 0 0 + 6 0 0 0 0 +N 7 0 0 0 3 6 4 6 6 1 + 6 4 6 6 1 + 1 1 0 0 0 +# +# cation definitions +# +# +CL 17 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +#OG 8 0 0 0 2 6 4 0 0 0 +# 6 4 0 0 0 +# 0 0 0 0 0 +End +# + + diff --git a/src/data/amber_q/coc.frg b/src/data/amber_q/coc.frg new file mode 100644 index 0000000..6e6de69 --- /dev/null +++ b/src/data/amber_q/coc.frg @@ -0,0 +1,14 @@ +# Fragment definition for crown ether fragment -CH2-O-CH2- +$coc + 7 1 1 0 +coc + 1 C1 CT 3 0 0 1 1 0.000000 0.000000 + 22H1 H1 0 0 0 1 1 0.150000 0.000000 + 33H1 H1 0 0 0 1 1 0.150000 0.000000 + 4 O OS 0 0 0 1 1 -0.600000 0.000000 + 5 C2 CT 4 0 0 1 1 0.000000 0.000000 + 62H2 H1 0 0 0 1 1 0.150000 0.000000 + 73H2 H1 0 0 0 1 1 0.150000 0.000000 + 1 4 5 + 2 1 3 + 6 5 7 diff --git a/src/data/amber_q/etl.frg b/src/data/amber_q/etl.frg new file mode 100644 index 0000000..8999e8a --- /dev/null +++ b/src/data/amber_q/etl.frg @@ -0,0 +1,16 @@ +# Fragment definition for ethanol +$ethanol + 9 1 1 0 +ethano + 1 C1 CT 0 0 0 1 1 -0.180000 0.000000 + 22H1 HC 0 0 0 1 1 0.060000 0.000000 + 33H1 HC 0 0 0 1 1 0.060000 0.000000 + 44H1 HC 0 0 0 1 1 0.060000 0.000000 + 5 C2 CT 0 0 0 1 1 -0.032000 0.000000 + 62H2 H1 0 0 0 1 1 0.148500 0.000000 + 73H2 H1 0 0 0 1 1 0.148500 0.000000 + 8 O OH 0 0 0 1 1 -0.700000 0.000000 + 9 H HO 0 0 0 1 1 0.435000 0.000000 + 2 1 3 + 4 1 5 8 9 + 6 5 7 diff --git a/src/data/amber_q/ions.par b/src/data/amber_q/ions.par new file mode 100644 index 0000000..38ff4ca --- /dev/null +++ b/src/data/amber_q/ions.par @@ -0,0 +1,145 @@ +#This is the AMBER99 standard parameter file for NWChem 4.0 +# +# Specific Parameters +# +# Automatically generated file /home/d3j191/ions.par +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +# +Atoms +U 238.03000 8.78640E-01 1.66120E-01 1 1111111111 + 92 4.39320E-01 1.66120E-01 +OU 16.00000 8.78640E-01 1.66120E-01 1 1111111111 + 8 4.39320E-01 1.66120E-01 +M11 22.98977 1.00000E-04 1.00000E-01 1 1111111111 + 11 1.00000E-04 1.00000E-01 +M21 22.98977 1.00000E-01 1.00000E-01 1 1111111111 + 11 1.00000E-01 1.00000E-01 +M12 22.98977 1.00000E-04 1.50000E-01 1 1111111111 + 11 1.00000E-04 1.50000E-01 +M22 22.98977 1.00000E-01 1.50000E-01 1 1111111111 + 11 1.00000E-01 1.50000E-01 +M13 22.98977 1.00000E-04 2.00000E-01 1 1111111111 + 11 1.00000E-04 2.00000E-01 +M23 22.98977 1.00000E-01 2.00000E-01 1 1111111111 + 11 1.00000E-01 2.00000E-01 +M14 22.98977 1.00000E-04 2.50000E-01 1 1111111111 + 11 1.00000E-04 2.50000E-01 +M24 22.98977 1.00000E-01 2.50000E-01 1 1111111111 + 11 1.00000E-01 2.50000E-01 +M15 22.98977 1.00000E-04 3.00000E-01 1 1111111111 + 11 1.00000E-04 3.00000E-01 +M25 22.98977 1.00000E-01 3.00000E-01 1 1111111111 + 11 1.00000E-01 3.00000E-01 +M16 22.98977 1.00000E-04 3.50000E-01 1 1111111111 + 11 1.00000E-04 3.50000E-01 +M26 22.98977 1.00000E-01 3.50000E-01 1 1111111111 + 11 1.00000E-01 3.50000E-01 +M17 22.98977 1.00000E-04 4.00000E-01 1 1111111111 + 11 1.00000E-04 4.00000E-01 +M27 22.98977 1.00000E-01 4.00000E-01 1 1111111111 + 11 1.00000E-01 4.00000E-01 +M18 22.98977 1.00000E-04 4.50000E-01 1 1111111111 + 11 1.00000E-04 4.50000E-01 +M28 22.98977 1.00000E-01 4.50000E-01 1 1111111111 + 11 1.00000E-01 4.50000E-01 +M19 22.98977 1.00000E-04 5.00000E-01 1 1111111111 + 11 1.00000E-04 5.00000E-01 +M29 22.98977 1.00000E-01 5.00000E-01 1 1111111111 + 11 1.00000E-01 5.00000E-01 +Cross +Bonds +U -OU 0.14100 2.67776E+05 0.000000 +Angles +OU -U -OU 2.09440 4.18400E+02 +Proper dihedrals +Improper dihedrals +Atom types +# +# Definition of the atom types +# +# This file contains the definition of AMBER atom types in terms of number and +# type of neighbor atoms. +# +# Note that the order in which the definitions are given is important. +# For each atom the last applicable entry in this file will be used, i.e. +# atom type definitions are given in increasing specificity. +# +# Atomic number increased by 200 means singly protonated +# 400 doubly +# 600 triply +# 800 un-protonated +# 1000 one non-hydrogen +# 2000 two non-hydrogens +# 3000 three non-hydrogens +# 4000 four non-hydrogens +# +# Atom number 3500 would signify any unprotonated atom with three non-hydrogens +# +# +# Each entry contains: +# +# 1 a4 atom type name +# +# 2 i7 atomic number +# +# 3 i3 atom saturation : 0 = undetermined, always applies +# 1 = aliphatic; +# 2 = double bond; +# 3 = aromatic; +# +# 4 i5 aliphatic ring : -1 = not in aliphatic ring +# 0 = any +# 1 = in at least one aliphatic ring +# 3 = in 3-membered aliphatic ring +# 4 = in 4-membered aliphatic ring +# 5 = in 5-membered aliphatic ring +# 6 = in 6-membered aliphatic ring +# 56 = junction 5 & 6 membered aliphatic rings +# 66 = junction two 6 membered aliphatic rings +# +# 5 i5 aromatic ring : -1 = not in aromatic ring +# 0 = any +# 1 = in at least one aromatic ring +# 5 = in 5-membered aromatic ring +# 6 = in 6-membered aromatic ring +# 56 = junction 5 & 6 membered aromatic rings +# 66 = junction two 6 membered aromatic rings +# 666 = junction three 6 membered aromatic rings +# +# 6 i3 number of neighbors : -1 = no neighbors +# 0 = any number of neighbors +# +# 7 i7 atom num neighbor 1 +# +# 8 i3 num n1 neighbors 0 = any number of neighbors +# +# 9 i7 atom num neighb n11 +# +# 10 i7 atom num neighb n12 +# +# 11 i7 atom num neighb n13 +# +# 12 i7 atom num neighbor 2 +# +# 13 i3 num n2 neighbors 0 = any number of neighbors +# +# 14 i7 atom num neighb n21 +# +# 15 i7 atom num neighb n22 +# +# 16 i7 atom num neighb n23 +# +# 17 i7 atom num neighbor 3 +# +# 18 i3 num n3 neighbors 0 = any number of neighbors +# +# 19 i7 atom num neighb n31 +# +# 20 i7 atom num neighb n32 +# +# 21 i7 atom num neighb n33 +# +# +End diff --git a/src/data/amber_q/lps_Pa/BTH.frg b/src/data/amber_q/lps_Pa/BTH.frg new file mode 100644 index 0000000..be37cbc --- /dev/null +++ b/src/data/amber_q/lps_Pa/BTH.frg @@ -0,0 +1,28 @@ +# This is an automatically generated fragment file +# +$BTH + 12 1 1 0 +BTH + 1 C1 CT 3 0 0 1 1 -0.021034 0.000000 + 22H1 HC 0 0 0 1 1 0.010517 0.000000 + 33H1 HC 0 0 0 1 1 0.010517 0.000000 + 4 C2 CT 0 0 0 1 1 -0.012697 0.000000 + 52H2 HC 0 0 0 1 1 0.006349 0.000000 + 63H2 HC 0 0 0 1 1 0.006349 0.000000 + 7 C3 CT 0 0 0 1 1 -0.024254 0.000000 + 82H3 HC 0 0 0 1 1 0.012127 0.000000 + 93H3 HC 0 0 0 1 1 0.012127 0.000000 + 10 C4 CT 4 0 0 1 1 -0.010029 0.000000 + 112H4 HC 0 0 0 1 1 0.005014 0.000000 + 123H4 HC 0 0 0 1 1 0.005014 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 diff --git a/src/data/amber_q/lps_Pa/BTH.sgm b/src/data/amber_q/lps_Pa/BTH.sgm new file mode 100644 index 0000000..5d8c10c --- /dev/null +++ b/src/data/amber_q/lps_Pa/BTH.sgm @@ -0,0 +1,129 @@ +# This is an automatically generated segment file +# + 4.600000 + 12 11 18 21 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.100000 0.000000 + 22H1 0 0 0 1 1 + HC 0.050000 0.000000 + 33H1 0 0 0 1 1 + HC 0.050000 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 4 0 0 1 1 + CT -0.100000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 4 5 0 0 + 0.000000 0.00000E+00 + 5 1 4 6 0 0 + 0.000000 0.00000E+00 + 6 1 4 7 0 0 + 0.000000 0.00000E+00 + 7 5 4 6 0 0 + 0.000000 0.00000E+00 + 8 5 4 7 0 0 + 0.000000 0.00000E+00 + 9 6 4 7 0 0 + 0.000000 0.00000E+00 + 10 4 7 8 0 0 + 0.000000 0.00000E+00 + 11 4 7 9 0 0 + 0.000000 0.00000E+00 + 12 4 7 10 0 0 + 0.000000 0.00000E+00 + 13 8 7 9 0 0 + 0.000000 0.00000E+00 + 14 8 7 10 0 0 + 0.000000 0.00000E+00 + 15 9 7 10 0 0 + 0.000000 0.00000E+00 + 16 7 10 11 0 0 + 0.000000 0.00000E+00 + 17 7 10 12 0 0 + 0.000000 0.00000E+00 + 18 11 10 12 0 0 + 0.000000 0.00000E+00 + 1 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 8 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 9 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 10 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 17 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 18 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 19 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 20 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 21 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/BTO.frg b/src/data/amber_q/lps_Pa/BTO.frg new file mode 100644 index 0000000..5e0d4fe --- /dev/null +++ b/src/data/amber_q/lps_Pa/BTO.frg @@ -0,0 +1,26 @@ +# This is an automatically generated fragment file +# +$BTO + 11 1 1 0 +BTO + 1 C1 C 3 1 0 1 1 0.190650 0.000000 + 2 O1 O2 0 0 0 1 1 -0.340348 0.000000 + 3 C2 CT 0 0 0 1 1 -0.043202 0.000000 + 42H2 HC 0 0 0 1 1 0.059487 0.000000 + 53H2 HC 0 0 0 1 1 0.059487 0.000000 + 6 C3 CT 0 0 0 1 1 0.014628 0.000000 + 72H3 HC 0 0 0 1 1 0.039814 0.000000 + 83H3 HC 0 0 0 1 1 0.039814 0.000000 + 9 C4 CT 4 0 0 1 1 -0.003054 0.000000 + 102H4 HC 0 0 0 1 1 -0.008638 0.000000 + 113H4 HC 0 0 0 1 1 -0.008638 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 diff --git a/src/data/amber_q/lps_Pa/BTO.sgm b/src/data/amber_q/lps_Pa/BTO.sgm new file mode 100644 index 0000000..8db7459 --- /dev/null +++ b/src/data/amber_q/lps_Pa/BTO.sgm @@ -0,0 +1,115 @@ +# This is an automatically generated segment file +# + 4.600000 + 11 10 16 18 0 0 1 1 + 0.000000 + 1 C1 3 1 0 1 1 + C 0.325525 0.000000 + 2 O1 0 0 0 1 1 + O2 -0.406899 0.000000 + 3 C2 0 0 0 1 1 + CT -0.111850 0.000000 + 42H2 0 0 0 1 1 + HC 0.096612 0.000000 + 53H2 0 0 0 1 1 + HC 0.096612 0.000000 + 6 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 72H3 0 0 0 1 1 + HC 0.050000 0.000000 + 83H3 0 0 0 1 1 + HC 0.050000 0.000000 + 9 C4 4 0 0 1 1 + CT -0.100000 0.000000 + 102H4 0 0 0 1 1 + HC 0.050000 0.000000 + 113H4 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 6 0 0 + 0.000000 0.00000E+00 + 6 6 7 0 0 + 0.000000 0.00000E+00 + 7 6 8 0 0 + 0.000000 0.00000E+00 + 8 6 9 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 10 9 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 6 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 6 0 0 + 0.000000 0.00000E+00 + 7 5 3 6 0 0 + 0.000000 0.00000E+00 + 8 3 6 7 0 0 + 0.000000 0.00000E+00 + 9 3 6 8 0 0 + 0.000000 0.00000E+00 + 10 3 6 9 0 0 + 0.000000 0.00000E+00 + 11 7 6 8 0 0 + 0.000000 0.00000E+00 + 12 7 6 9 0 0 + 0.000000 0.00000E+00 + 13 8 6 9 0 0 + 0.000000 0.00000E+00 + 14 6 9 10 0 0 + 0.000000 0.00000E+00 + 15 6 9 11 0 0 + 0.000000 0.00000E+00 + 16 10 9 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 6 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 6 7 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 6 8 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 6 9 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 6 7 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 6 8 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 6 9 0 0 + 0 0.000000 0.00000E+00 + 10 5 3 6 7 0 0 + 0 0.000000 0.00000E+00 + 11 5 3 6 8 0 0 + 0 0.000000 0.00000E+00 + 12 5 3 6 9 0 0 + 0 0.000000 0.00000E+00 + 13 3 6 9 10 0 0 + 0 0.000000 0.00000E+00 + 14 3 6 9 11 0 0 + 0 0.000000 0.00000E+00 + 15 7 6 9 10 0 0 + 0 0.000000 0.00000E+00 + 16 7 6 9 11 0 0 + 0 0.000000 0.00000E+00 + 17 8 6 9 10 0 0 + 0 0.000000 0.00000E+00 + 18 8 6 9 11 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/BUT.frg b/src/data/amber_q/lps_Pa/BUT.frg new file mode 100644 index 0000000..e763e5f --- /dev/null +++ b/src/data/amber_q/lps_Pa/BUT.frg @@ -0,0 +1,30 @@ +# This is an automatically generated fragment file +# +$BUT + 13 1 1 0 +BUT + 1 C1 CT 3 0 0 1 1 -0.011176 0.000000 + 22H1 HC 0 0 0 1 1 0.005588 0.000000 + 33H1 HC 0 0 0 1 1 0.005588 0.000000 + 4 C2 CT 0 0 0 1 1 -0.023686 0.000000 + 52H2 HC 0 0 0 1 1 0.011843 0.000000 + 63H2 HC 0 0 0 1 1 0.011843 0.000000 + 7 C3 CT 0 0 0 1 1 -0.006136 0.000000 + 82H3 HC 0 0 0 1 1 0.003068 0.000000 + 93H3 HC 0 0 0 1 1 0.003068 0.000000 + 10 C4 CT 0 0 0 1 1 0.091023 0.000000 + 112H4 HC 0 0 0 1 1 -0.030341 0.000000 + 123H4 HC 0 0 0 1 1 -0.030341 0.000000 + 134H4 HC 0 0 0 1 1 -0.030341 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 diff --git a/src/data/amber_q/lps_Pa/BUT.sgm b/src/data/amber_q/lps_Pa/BUT.sgm new file mode 100644 index 0000000..d6fa8b7 --- /dev/null +++ b/src/data/amber_q/lps_Pa/BUT.sgm @@ -0,0 +1,145 @@ +# This is an automatically generated segment file +# + 4.600000 + 13 12 21 24 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.100000 0.000000 + 22H1 0 0 0 1 1 + HC 0.050000 0.000000 + 33H1 0 0 0 1 1 + HC 0.050000 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 0 0 0 1 1 + CT -0.150000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 134H4 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 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0000000..09962af --- /dev/null +++ b/src/data/amber_q/lps_Pa/GA3.frg @@ -0,0 +1,65 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GA3 + 29 1 1 0 +GA3 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.020000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 C3 CT 0 0 0 1 1 0.250000 0.000000 + 7 H3 H1 0 0 0 1 1 0.050000 0.000000 + 8 O3 OG 4 0 0 1 1 -0.300000 0.000000 + 9 C4 CT 0 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 0 1 1 0.050000 0.000000 + 11 O4 OG 5 0 0 1 1 -0.300000 0.000000 + 12 C5 CT 0 0 0 1 1 0.250000 0.000000 + 13 H5 H1 0 0 0 1 1 0.050000 0.000000 + 14 C6 CT 0 0 0 1 1 0.200000 0.000000 + 152H6 H1 0 0 0 1 1 0.050000 0.000000 + 163H6 H1 0 0 0 1 1 0.050000 0.000000 + 17 O6 OH 0 0 0 1 1 -0.490000 0.000000 + 18 HO6 HO 0 0 0 1 1 0.190000 0.000000 + 19 N N 0 0 0 1 1 -0.410000 0.000000 + 20 HN H 0 0 0 1 1 0.270000 0.000000 + 21 CA CT 0 0 0 1 1 0.020000 0.000000 + 22 HA H1 0 0 0 1 1 0.050000 0.000000 + 23 CB CT 0 0 0 1 1 -0.150000 0.000000 + 242HB HC 0 0 0 1 1 0.050000 0.000000 + 253HB HC 0 0 0 1 1 0.050000 0.000000 + 264HB HC 0 0 0 1 1 0.050000 0.000000 + 27 C C 0 1 0 1 1 0.800000 0.000000 + 28 OC O2 0 0 0 1 1 -0.900000 0.000000 + 29 O O2 0 0 0 1 1 -0.900000 0.000000 + 1 2 + 1 3 + 1 4 + 3 12 + 4 5 + 4 6 + 4 19 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 14 15 + 14 16 + 14 17 + 17 18 + 19 20 + 19 21 + 21 22 + 21 23 + 21 27 + 23 24 + 23 25 + 23 26 + 27 28 + 27 29 diff --git a/src/data/amber_q/lps_Pa/GA3.sgm b/src/data/amber_q/lps_Pa/GA3.sgm new file mode 100644 index 0000000..fc3d43c --- /dev/null +++ b/src/data/amber_q/lps_Pa/GA3.sgm @@ -0,0 +1,383 @@ +# This is an automatically generated segment file +# + 4.600000 + 29 29 53 77 1 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC 0.038921 0.000000 + 2 H1 0 0 0 1 1 + H2 0.186521 0.000000 + 3 OR 0 0 0 1 1 + 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0.000000 0.00000E+00 + 45 14 12 16 1 0 0 + 0 0.000000 0.00000E+00 + 46 14 12 16 17 0 0 + 0 0.000000 0.00000E+00 + 47 14 12 16 18 0 0 + 0 0.000000 0.00000E+00 + 48 1 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 49 1 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 50 1 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 51 12 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 52 12 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 53 12 16 18 21 0 0 + 0 0.000000 0.00000E+00 + 54 17 16 18 19 0 0 + 0 0.000000 0.00000E+00 + 55 17 16 18 20 0 0 + 0 0.000000 0.00000E+00 + 56 17 16 18 21 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/GL4.frg b/src/data/amber_q/lps_Pa/GL4.frg new file mode 100644 index 0000000..5377d35 --- /dev/null +++ b/src/data/amber_q/lps_Pa/GL4.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL4 + 21 1 1 0 +GL4 + 1 C1 EC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 0 1 1 0.050000 0.000000 + 21 O6 OG 4 0 0 1 1 -0.300000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 diff --git a/src/data/amber_q/lps_Pa/GL4.sgm b/src/data/amber_q/lps_Pa/GL4.sgm new file mode 100644 index 0000000..2cad33b --- /dev/null +++ b/src/data/amber_q/lps_Pa/GL4.sgm @@ -0,0 +1,275 @@ +# This is an automatically generated segment file +# + 4.600000 + 21 21 37 56 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + EC 0.041291 0.000000 + 2 H1 0 0 0 1 1 + H2 0.170645 0.000000 + 3 OR 0 0 0 1 1 + OS -0.365330 0.000000 + 4 C2 0 0 0 1 1 + CT 0.081809 0.000000 + 5 H2 0 0 0 1 1 + H1 0.162189 0.000000 + 6 O2 0 0 0 1 1 + OH -0.599983 0.000000 + 7 HO2 0 0 0 1 1 + HO 0.340524 0.000000 + 8 C3 0 0 0 1 1 + CT 0.078232 0.000000 + 9 H3 0 0 0 1 1 + H1 0.160184 0.000000 + 10 O3 0 0 0 1 1 + OH -0.605072 0.000000 + 11 HO3 0 0 0 1 1 + HO 0.409833 0.000000 + 12 C4 0 0 0 1 1 + CT 0.095775 0.000000 + 13 H4 0 0 0 1 1 + H1 0.136486 0.000000 + 14 O4 0 0 0 1 1 + OH -0.634070 0.000000 + 15 HO4 0 0 0 1 1 + HO 0.467736 0.000000 + 16 C5 0 0 0 1 1 + CT 0.010339 0.000000 + 17 H5 0 0 0 1 1 + H1 0.151057 0.000000 + 18 C6 0 0 0 1 1 + CT -0.014409 0.000000 + 192H6 0 0 0 1 1 + H1 0.104895 0.000000 + 203H6 0 0 0 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fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL5 + 22 1 1 0 +GL5 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 0 1 1 0.050000 0.000000 + 21 O6 OH 0 0 0 1 1 -0.490000 0.000000 + 22 HO6 HO 0 0 0 1 1 0.190000 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0.050000 0.000000 + 10 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 0 1 1 0.200000 0.000000 + 19 O6 OG 4 0 0 1 1 -0.300000 0.000000 + 202H6 H1 0 0 0 1 1 0.050000 0.000000 + 213H6 H1 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 diff --git a/src/data/amber_q/lps_Pa/GL6.sgm b/src/data/amber_q/lps_Pa/GL6.sgm new file mode 100644 index 0000000..36522f9 --- /dev/null +++ b/src/data/amber_q/lps_Pa/GL6.sgm @@ -0,0 +1,275 @@ +# This is an automatically generated segment file +# + 4.600000 + 21 21 37 56 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + EC 0.043199 0.000000 + 2 H1 0 0 0 1 1 + H2 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--git a/src/data/amber_q/lps_Pa/HDH.frg b/src/data/amber_q/lps_Pa/HDH.frg new file mode 100644 index 0000000..a3a4290 --- /dev/null +++ b/src/data/amber_q/lps_Pa/HDH.frg @@ -0,0 +1,34 @@ +# This is an automatically generated fragment file +# +$HDH + 15 1 1 0 +HDH + 1 C1 C 3 1 0 1 1 0.597879 0.000000 + 2 O1 O 0 0 0 1 1 -0.656819 0.000000 + 3 C2 CT 0 0 0 1 1 -0.065272 0.000000 + 42H2 HC 0 0 0 1 1 0.032636 0.000000 + 53H2 HC 0 0 0 1 1 0.032636 0.000000 + 6 C3 CT 0 0 0 1 1 0.378592 0.000000 + 7 H3 H1 0 0 0 1 1 -0.030998 0.000000 + 8 O3 OH 0 0 0 1 1 -0.686049 0.000000 + 9 HO3 HO 0 0 0 1 1 0.397395 0.000000 + 10 C4 CT 0 0 0 1 1 0.001626 0.000000 + 112H4 HC 0 0 0 1 1 -0.000813 0.000000 + 123H4 HC 0 0 0 1 1 -0.000813 0.000000 + 13 C5 CT 4 0 0 1 1 -0.021174 0.000000 + 142H5 HC 0 0 0 1 1 0.010587 0.000000 + 153H5 HC 0 0 0 1 1 0.010587 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 10 + 8 9 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 diff --git a/src/data/amber_q/lps_Pa/HDH.sgm 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b/src/data/amber_q/lps_Pa/HP4.frg new file mode 100644 index 0000000..03eef07 --- /dev/null +++ b/src/data/amber_q/lps_Pa/HP4.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HP4 + 20 1 1 0 +HP4 + 1 C1 AC 0 0 0 1 1 0.000000 0.000000 + 2 O1 OG 3 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 4 0 0 1 1 -0.050000 0.000000 + 5 H2 H2 0 0 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 0 1 1 0.250000 0.000000 + 7 H3 H1 0 0 0 1 1 0.050000 0.000000 + 8 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 9 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 10 C4 CT 5 0 0 1 1 -0.050000 0.000000 + 11 H4 H1 0 0 0 1 1 0.050000 0.000000 + 12 O4 OG 6 0 0 1 1 -0.300000 0.000000 + 13 C5 CT 0 0 0 1 1 0.250000 0.000000 + 14 H5 H1 0 0 0 1 1 0.050000 0.000000 + 15 C6 CT 7 0 0 1 1 -0.050000 0.000000 + 16 H6 H1 0 0 0 1 1 0.050000 0.000000 + 17 C7 CT 0 0 0 1 1 0.200000 0.000000 + 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0 0.000000 0.00000E+00 + 1 29 24 25 28 0 0 + 0 0.000000 0.00000E+00 + 2 25 26 29 27 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/KD4.frg b/src/data/amber_q/lps_Pa/KD4.frg new file mode 100644 index 0000000..55afd7d --- /dev/null +++ b/src/data/amber_q/lps_Pa/KD4.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$KD4 + 24 1 1 0 +KD4 + 1 C1 C 0 1 0 1 1 0.800000 0.000000 + 2 O1 O2 0 0 0 1 1 -0.900000 0.000000 + 3 O O2 0 0 0 1 1 -0.900000 0.000000 + 4 OR OS 0 0 0 1 1 -0.300000 0.000000 + 5 C2 AC 3 0 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 0 1 1 -0.100000 0.000000 + 72H3 HC 0 0 0 1 1 0.050000 0.000000 + 83H3 HC 0 0 0 1 1 0.050000 0.000000 + 9 C4 CT 0 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 0 1 1 0.050000 0.000000 + 11 O4 OG 4 0 0 1 1 -0.300000 0.000000 + 12 C5 CT 5 0 0 1 1 -0.050000 0.000000 + 13 H5 H1 0 0 0 1 1 0.050000 0.000000 + 14 C6 CT 0 0 0 1 1 0.250000 0.000000 + 15 H6 H1 0 0 0 1 1 0.050000 0.000000 + 16 C7 CT 0 0 0 1 1 0.250000 0.000000 + 17 H7 H1 0 0 0 1 1 0.050000 0.000000 + 18 O7 OH 0 0 0 1 1 -0.490000 0.000000 + 19 HO7 HO 0 0 0 1 1 0.190000 0.000000 + 20 C8 CT 0 0 0 1 1 0.200000 0.000000 + 212H8 H1 0 0 0 1 1 0.050000 0.000000 + 223H8 H1 0 0 0 1 1 0.050000 0.000000 + 23 O8 OH 0 0 0 1 1 -0.490000 0.000000 + 24 HO8 HO 0 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 14 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 23 + 23 24 diff --git a/src/data/amber_q/lps_Pa/KD4.sgm b/src/data/amber_q/lps_Pa/KD4.sgm new file mode 100644 index 0000000..ea87111 --- /dev/null +++ b/src/data/amber_q/lps_Pa/KD4.sgm @@ -0,0 +1,307 @@ +# This is an automatically generated segment file +# + 4.600000 + 24 24 42 60 1 0 1 1 + 0.000000 + 1 C1 0 1 0 1 1 + C 0.473407 0.000000 + 2 O1 0 0 0 1 1 + O2 -0.736704 0.000000 + 3 O 0 0 0 1 1 + O2 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0.000000 0.00000E+00 + 68 21 19 23 25 0 0 + 0 0.000000 0.00000E+00 + 69 21 19 23 26 0 0 + 0 0.000000 0.00000E+00 + 70 19 23 26 27 0 0 + 0 0.000000 0.00000E+00 + 71 24 23 26 27 0 0 + 0 0.000000 0.00000E+00 + 72 25 23 26 27 0 0 + 0 0.000000 0.00000E+00 + 1 5 3 1 2 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/PET.frg b/src/data/amber_q/lps_Pa/PET.frg new file mode 100644 index 0000000..32fef1d --- /dev/null +++ b/src/data/amber_q/lps_Pa/PET.frg @@ -0,0 +1,38 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$PET + 16 1 1 0 +PET + 1 C1 CT 3 0 0 1 1 -0.100000 0.000000 + 22H1 HC 0 0 0 1 1 0.050000 0.000000 + 33H1 HC 0 0 0 1 1 0.050000 0.000000 + 4 C2 CT 0 0 0 1 1 -0.100000 0.000000 + 52H2 HC 0 0 0 1 1 0.050000 0.000000 + 63H2 HC 0 0 0 1 1 0.050000 0.000000 + 7 C3 CT 0 0 0 1 1 -0.100000 0.000000 + 82H3 HC 0 0 0 1 1 0.050000 0.000000 + 93H3 HC 0 0 0 1 1 0.050000 0.000000 + 10 C4 CT 0 0 0 1 1 -0.100000 0.000000 + 112H4 HC 0 0 0 1 1 0.050000 0.000000 + 123H4 HC 0 0 0 1 1 0.050000 0.000000 + 13 C5 CT 0 0 0 1 1 -0.150000 0.000000 + 142H5 HC 0 0 0 1 1 0.050000 0.000000 + 153H5 HC 0 0 0 1 1 0.050000 0.000000 + 164H5 HC 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 diff --git a/src/data/amber_q/lps_Pa/PET.sgm b/src/data/amber_q/lps_Pa/PET.sgm new file mode 100644 index 0000000..5f5d6cb --- /dev/null +++ b/src/data/amber_q/lps_Pa/PET.sgm @@ -0,0 +1,187 @@ +# This is an automatically generated segment file +# + 4.600000 + 16 15 27 33 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + CT -0.026814 0.000000 + 22H1 0 0 0 1 1 + HC 0.013407 0.000000 + 33H1 0 0 0 1 1 + HC 0.013407 0.000000 + 4 C2 0 0 0 1 1 + CT -0.100000 0.000000 + 52H2 0 0 0 1 1 + HC 0.050000 0.000000 + 63H2 0 0 0 1 1 + HC 0.050000 0.000000 + 7 C3 0 0 0 1 1 + CT -0.100000 0.000000 + 82H3 0 0 0 1 1 + HC 0.050000 0.000000 + 93H3 0 0 0 1 1 + HC 0.050000 0.000000 + 10 C4 0 0 0 1 1 + CT -0.100000 0.000000 + 112H4 0 0 0 1 1 + HC 0.050000 0.000000 + 123H4 0 0 0 1 1 + HC 0.050000 0.000000 + 13 C5 0 0 0 1 1 + CT -0.150000 0.000000 + 142H5 0 0 0 1 1 + HC 0.050000 0.000000 + 153H5 0 0 0 1 1 + HC 0.050000 0.000000 + 164H5 0 0 0 1 1 + HC 0.050000 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 4 5 0 0 + 0.000000 0.00000E+00 + 5 4 6 0 0 + 0.000000 0.00000E+00 + 6 4 7 0 0 + 0.000000 0.00000E+00 + 7 7 8 0 0 + 0.000000 0.00000E+00 + 8 7 9 0 0 + 0.000000 0.00000E+00 + 9 7 10 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 12 10 13 0 0 + 0.000000 0.00000E+00 + 13 13 14 0 0 + 0.000000 0.00000E+00 + 14 13 15 0 0 + 0.000000 0.00000E+00 + 15 13 16 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 4 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0.000000 0.00000E+00 + 3 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 8 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 9 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 10 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 17 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 18 4 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 19 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 20 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 21 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 22 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 24 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 25 7 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 26 7 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 27 7 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 28 11 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 29 11 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 30 11 10 13 16 0 0 + 0 0.000000 0.00000E+00 + 31 12 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 32 12 10 13 15 0 0 + 0 0.000000 0.00000E+00 + 33 12 10 13 16 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/PO4.frg b/src/data/amber_q/lps_Pa/PO4.frg new file mode 100644 index 0000000..619f3e1 --- /dev/null +++ b/src/data/amber_q/lps_Pa/PO4.frg @@ -0,0 +1,14 @@ +# This is an automatically generated fragment file +# +$PO4 + 5 1 1 0 +PO4 + 1 OP1 OS 3 0 0 1 1 -0.139474 0.000000 + 2 P P 0 0 0 1 1 0.938933 0.000000 + 3 OP2 O2 0 0 0 1 1 -0.933153 0.000000 + 4 OP3 O2 0 0 0 1 1 -0.933153 0.000000 + 5 OP4 O2 0 0 0 1 1 -0.933153 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 diff --git a/src/data/amber_q/lps_Pa/PO4.sgm b/src/data/amber_q/lps_Pa/PO4.sgm new file mode 100644 index 0000000..0436063 --- /dev/null +++ b/src/data/amber_q/lps_Pa/PO4.sgm @@ -0,0 +1,35 @@ +# This is an automatically generated segment file +# + 4.600000 + 5 4 6 0 0 0 1 1 + 0.000000 + 1 OP1 3 0 0 1 1 + OS -0.139474 0.000000 + 2 P 0 0 0 1 1 + P 0.938933 0.000000 + 3 OP2 0 0 0 1 1 + O2 -0.933153 0.000000 + 4 OP3 0 0 0 1 1 + O2 -0.933153 0.000000 + 5 OP4 0 0 0 1 1 + O2 -0.933153 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 2 3 0 0 + 0.000000 0.00000E+00 + 3 2 4 0 0 + 0.000000 0.00000E+00 + 4 2 5 0 0 + 0.000000 0.00000E+00 + 1 1 2 3 0 0 + 0.000000 0.00000E+00 + 2 1 2 4 0 0 + 0.000000 0.00000E+00 + 3 1 2 5 0 0 + 0.000000 0.00000E+00 + 4 3 2 4 0 0 + 0.000000 0.00000E+00 + 5 3 2 5 0 0 + 0.000000 0.00000E+00 + 6 4 2 5 0 0 + 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_Pa/RH2.frg b/src/data/amber_q/lps_Pa/RH2.frg new file mode 100644 index 0000000..6d7ce2c --- /dev/null +++ b/src/data/amber_q/lps_Pa/RH2.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$RH2 + 20 1 1 0 +RH2 + 1 C1 AC 3 0 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 0 1 1 0.050000 0.000000 + 6 O2 OG 4 0 0 1 1 -0.300000 0.000000 + 7 C3 CT 0 0 0 1 1 0.250000 0.000000 + 8 H3 H1 0 0 0 1 1 0.050000 0.000000 + 9 O3 OH 0 0 0 1 1 -0.490000 0.000000 + 10 HO3 HO 0 0 0 1 1 0.190000 0.000000 + 11 C4 CT 0 0 0 1 1 0.250000 0.000000 + 12 H4 H1 0 0 0 1 1 0.050000 0.000000 + 13 O4 OH 0 0 0 1 1 -0.490000 0.000000 + 14 HO4 HO 0 0 0 1 1 0.190000 0.000000 + 15 C5 CT 0 0 0 1 1 0.250000 0.000000 + 16 H5 H1 0 0 0 1 1 0.050000 0.000000 + 17 C6 CT 0 0 0 1 1 -0.150000 0.000000 + 182H6 HC 0 0 0 1 1 0.050000 0.000000 + 193H6 HC 0 0 0 1 1 0.050000 0.000000 + 204H6 HC 0 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/lps_Pa/RH2.sgm b/src/data/amber_q/lps_Pa/RH2.sgm new file mode 100644 index 0000000..7b6754c --- /dev/null +++ b/src/data/amber_q/lps_Pa/RH2.sgm @@ -0,0 +1,263 @@ +# This is an automatically generated segment file +# + 4.600000 + 20 20 36 53 0 0 1 1 + 0.000000 + 1 C1 3 0 0 1 1 + AC -0.207395 0.000000 + 2 H1 0 0 0 1 1 + H2 0.118124 0.000000 + 3 OR 0 0 0 1 1 + OS -0.192617 0.000000 + 4 C2 0 0 0 1 1 + CT -0.071635 0.000000 + 5 H2 0 0 0 1 1 + H1 0.157937 0.000000 + 6 O2 4 0 0 1 1 + OG -0.052212 0.000000 + 7 C3 0 0 0 1 1 + CT 0.232988 0.000000 + 8 H3 0 0 0 1 1 + H1 0.167022 0.000000 + 9 O3 0 0 0 1 1 + OH -0.680086 0.000000 + 10 HO3 0 0 0 1 1 + HO 0.402264 0.000000 + 11 C4 0 0 0 1 1 + CT 0.192216 0.000000 + 12 H4 0 0 0 1 1 + H1 0.062758 0.000000 + 13 O4 0 0 0 1 1 + OH -0.690913 0.000000 + 14 HO4 0 0 0 1 1 + HO 0.418323 0.000000 + 15 C5 0 0 0 1 1 + CT 0.087070 0.000000 + 16 H5 0 0 0 1 1 + H1 0.088853 0.000000 + 17 C6 0 0 0 1 1 + CT -0.261219 0.000000 + 182H6 0 0 0 1 1 + HC 0.076174 0.000000 + 193H6 0 0 0 1 1 + HC 0.076174 0.000000 + 204H6 0 0 0 1 1 + HC 0.076174 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 3 15 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 7 0 0 + 0.000000 0.00000E+00 + 8 7 8 0 0 + 0.000000 0.00000E+00 + 9 7 9 0 0 + 0.000000 0.00000E+00 + 10 7 11 0 0 + 0.000000 0.00000E+00 + 11 9 10 0 0 + 0.000000 0.00000E+00 + 12 11 12 0 0 + 0.000000 0.00000E+00 + 13 11 13 0 0 + 0.000000 0.00000E+00 + 14 11 15 0 0 + 0.000000 0.00000E+00 + 15 13 14 0 0 + 0.000000 0.00000E+00 + 16 15 16 0 0 + 0.000000 0.00000E+00 + 17 15 17 0 0 + 0.000000 0.00000E+00 + 18 17 18 0 0 + 0.000000 0.00000E+00 + 19 17 19 0 0 + 0.000000 0.00000E+00 + 20 17 20 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 3 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0.000000 0.00000E+00 + 18 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 19 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 20 6 4 7 11 0 0 + 0 0.000000 0.00000E+00 + 21 4 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 22 8 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 23 11 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 24 4 7 11 12 0 0 + 0 0.000000 0.00000E+00 + 25 4 7 11 13 0 0 + 0 0.000000 0.00000E+00 + 26 4 7 11 15 0 0 + 0 0.000000 0.00000E+00 + 27 8 7 11 12 0 0 + 0 0.000000 0.00000E+00 + 28 8 7 11 13 0 0 + 0 0.000000 0.00000E+00 + 29 8 7 11 15 0 0 + 0 0.000000 0.00000E+00 + 30 9 7 11 12 0 0 + 0 0.000000 0.00000E+00 + 31 9 7 11 13 0 0 + 0 0.000000 0.00000E+00 + 32 9 7 11 15 0 0 + 0 0.000000 0.00000E+00 + 33 7 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 34 12 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 35 15 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 36 7 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 37 7 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 38 7 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 39 12 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 40 12 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 41 12 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 42 13 11 15 3 0 0 + 0 0.000000 0.00000E+00 + 43 13 11 15 16 0 0 + 0 0.000000 0.00000E+00 + 44 13 11 15 17 0 0 + 0 0.000000 0.00000E+00 + 45 3 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 46 3 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 47 3 15 17 20 0 0 + 0 0.000000 0.00000E+00 + 48 11 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 49 11 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 50 11 15 17 20 0 0 + 0 0.000000 0.00000E+00 + 51 16 15 17 18 0 0 + 0 0.000000 0.00000E+00 + 52 16 15 17 19 0 0 + 0 0.000000 0.00000E+00 + 53 16 15 17 20 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_q/lps_ec/BU1.frg b/src/data/amber_q/lps_ec/BU1.frg new file mode 100644 index 0000000..1cf9d5b --- /dev/null +++ b/src/data/amber_q/lps_ec/BU1.frg @@ -0,0 +1,34 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$BU1 + 13 1 1 0 +BU1 + 1 C1 CT 3 0 0 1 1 -0.864254 0.000000 + 22H1 HC 0 0 0 1 1 0.349875 0.000000 + 33H1 HC 0 0 0 1 1 0.349875 0.000000 + 4 C2 CT 0 0 0 1 1 -0.223449 0.000000 + 52H2 HC 0 0 0 1 1 0.185394 0.000000 + 63H2 HC 0 0 0 1 1 0.185394 0.000000 + 7 C3 CT 0 0 0 1 1 -0.091103 0.000000 + 82H3 HC 0 0 0 1 1 0.019263 0.000000 + 93H3 HC 0 0 0 1 1 0.019263 0.000000 + 10 C4 CT 0 0 0 1 1 -0.066351 0.000000 + 112H4 HC 0 0 0 1 1 0.045364 0.000000 + 123H4 HC 0 0 0 1 1 0.045364 0.000000 + 134H4 HC 0 0 0 1 1 0.045364 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 diff --git a/src/data/amber_q/lps_ec/BU2.frg b/src/data/amber_q/lps_ec/BU2.frg new file mode 100644 index 0000000..b61690e --- /dev/null +++ b/src/data/amber_q/lps_ec/BU2.frg @@ -0,0 +1,32 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$BU2 + 12 1 1 0 +BU2 + 1 C1 CT 3 0 0 1 1 -0.263991 0.000000 + 22H1 HC 0 0 0 1 1 0.073152 0.000000 + 33H1 HC 0 0 0 1 1 0.073152 0.000000 + 4 C2 CT 0 0 0 1 1 0.035826 0.000000 + 52H2 HC 0 0 0 1 1 -0.119366 0.000000 + 63H2 HC 0 0 0 1 1 -0.119366 0.000000 + 7 C3 CT 0 0 0 1 1 0.107797 0.000000 + 82H3 HC 0 0 0 1 1 -0.024820 0.000000 + 93H3 HC 0 0 0 1 1 -0.024820 0.000000 + 10 C4 CT 4 0 0 1 1 -0.195478 0.000000 + 112H4 HC 0 0 0 1 1 0.228957 0.000000 + 123H4 HC 0 0 0 1 1 0.228957 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 diff --git a/src/data/amber_q/lps_ec/GA1.frg b/src/data/amber_q/lps_ec/GA1.frg new file mode 100644 index 0000000..5c27f05 --- /dev/null +++ b/src/data/amber_q/lps_ec/GA1.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GA1 + 23 1 1 0 +GA1 + 1 C1 AC 0 0 0 1 1 0.193194 0.000000 + 2 H1 H2 0 0 0 1 1 0.072590 0.000000 + 3 O1 OS 3 0 0 1 1 -0.087662 0.000000 + 4 C2 CT 0 0 0 1 1 0.299004 0.000000 + 5 H2 H1 0 0 0 1 1 0.069050 0.000000 + 6 O2 OH 0 0 0 1 1 -0.807938 0.000000 + 7 HO2 HO 0 0 0 1 1 0.452336 0.000000 + 8 C3 CT 0 0 0 1 1 0.726424 0.000000 + 9 H3 H1 0 0 0 1 1 -0.083389 0.000000 + 10 O3 OH 0 0 0 1 1 -1.291508 0.000000 + 11 HO3 HO 0 0 0 1 1 0.630135 0.000000 + 12 C4 CT 0 0 0 1 1 0.056284 0.000000 + 13 H4 H1 0 0 0 1 1 0.301851 0.000000 + 14 O4 OH 0 0 0 1 1 -1.000961 0.000000 + 15 HO4 HO 0 0 0 1 1 0.556479 0.000000 + 16 C5 CT 0 0 0 1 1 0.236298 0.000000 + 17 H5 H1 0 0 0 1 1 0.075909 0.000000 + 18 C6 CT 0 0 0 1 1 0.278215 0.000000 + 192H6 H1 0 0 0 1 1 0.092913 0.000000 + 203H6 H1 0 0 0 1 1 0.092913 0.000000 + 21 O6 OH 0 0 0 1 1 -0.759032 0.000000 + 22 HO6 HO 0 0 0 1 1 0.417351 0.000000 + 23 OR OS 0 0 0 1 1 -0.521455 0.000000 + 1 2 + 1 3 + 1 4 + 1 23 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 16 23 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/lps_ec/GL1.frg b/src/data/amber_q/lps_ec/GL1.frg new file mode 100644 index 0000000..ee054b0 --- /dev/null +++ b/src/data/amber_q/lps_ec/GL1.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GL1 + 19 1 1 0 +GL1 + 1 C1 AC 0 0 0 1 1 0.183946 0.000000 + 2 H1 H2 0 0 0 1 1 0.092269 0.000000 + 3 O1 OS 3 0 0 1 1 0.142115 0.000000 + 4 C2 CT 0 0 0 1 1 0.487700 0.000000 + 5 H2 H1 0 0 0 1 1 0.063090 0.000000 + 6 O2 OH 0 0 0 1 1 -1.053101 0.000000 + 7 HO2 HO 0 0 0 1 1 0.554009 0.000000 + 8 C3 CT 4 0 0 1 1 -0.301894 0.000000 + 9 H3 H1 0 0 0 1 1 0.098353 0.000000 + 10 C4 CT 0 0 0 1 1 0.606714 0.000000 + 11 H4 H1 0 0 0 1 1 -0.060495 0.000000 + 12 O4 OH 0 0 0 1 1 -0.833144 0.000000 + 13 HO4 HO 0 0 0 1 1 0.425334 0.000000 + 14 C5 CT 0 0 0 1 1 0.404266 0.000000 + 15 H5 H1 0 0 0 1 1 -0.166015 0.000000 + 16 C6 CT 5 0 0 1 1 -0.375243 0.000000 + 172H6 H1 0 0 0 1 1 0.142981 0.000000 + 183H6 H1 0 0 0 1 1 0.142981 0.000000 + 19 OR OS 0 0 0 1 1 -0.553867 0.000000 + 1 2 + 1 3 + 1 4 + 1 19 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 19 + 16 17 + 16 18 diff --git a/src/data/amber_q/lps_ec/GL2.frg b/src/data/amber_q/lps_ec/GL2.frg new file mode 100644 index 0000000..34bed82 --- /dev/null +++ b/src/data/amber_q/lps_ec/GL2.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GL2 + 21 1 1 0 +GL2 + 1 C1 AC 0 0 0 1 1 0.509726 0.000000 + 2 H1 H2 0 0 0 1 1 0.133252 0.000000 + 3 O1 OS 3 0 0 1 1 -0.231396 0.000000 + 4 C2 CT 4 0 0 1 1 -0.469045 0.000000 + 5 H2 H1 0 0 0 1 1 0.168614 0.000000 + 6 C3 CT 0 0 0 1 1 0.680179 0.000000 + 7 H3 H1 0 0 0 1 1 -0.069090 0.000000 + 8 O3 OH 0 0 0 1 1 -0.871026 0.000000 + 9 HO3 HO 0 0 0 1 1 0.465673 0.000000 + 10 C4 CT 0 0 0 1 1 0.305521 0.000000 + 11 H4 H1 0 0 0 1 1 0.099451 0.000000 + 12 O4 OH 0 0 0 1 1 -0.948886 0.000000 + 13 HO4 HO 0 0 0 1 1 0.531024 0.000000 + 14 C5 CT 0 0 0 1 1 0.419333 0.000000 + 15 H5 H1 0 0 0 1 1 0.004956 0.000000 + 16 C6 CT 0 0 0 1 1 0.267679 0.000000 + 172H6 H1 0 0 0 1 1 -0.031244 0.000000 + 183H6 H1 0 0 0 1 1 -0.031244 0.000000 + 19 O6 OH 0 0 0 1 1 -0.812945 0.000000 + 20 HO6 HO 0 0 0 1 1 0.486555 0.000000 + 21 OR OS 0 0 0 1 1 -0.607087 0.000000 + 1 2 + 1 3 + 1 4 + 1 21 + 4 5 + 4 6 + 6 7 + 6 8 + 6 10 + 8 9 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 21 + 16 17 + 16 18 + 16 19 + 19 20 diff --git a/src/data/amber_q/lps_ec/GL3.frg b/src/data/amber_q/lps_ec/GL3.frg new file mode 100644 index 0000000..bd50437 --- /dev/null +++ b/src/data/amber_q/lps_ec/GL3.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GL3 + 21 1 1 0 +GL3 + 1 C1 AC 0 0 0 1 1 0.573279 0.000000 + 2 H1 H2 0 0 0 1 1 0.108300 0.000000 + 3 O1 OS 3 0 0 1 1 -0.306364 0.000000 + 4 C2 CT 0 0 0 1 1 0.177942 0.000000 + 5 H2 H1 0 0 0 1 1 0.092618 0.000000 + 6 O2 OH 0 0 0 1 1 -0.718049 0.000000 + 7 HO2 HO 0 0 0 1 1 0.415211 0.000000 + 8 C3 CT 0 0 0 1 1 0.325435 0.000000 + 9 H3 H1 0 0 0 1 1 0.076482 0.000000 + 10 O3 OH 0 0 0 1 1 -0.795236 0.000000 + 11 HO3 HO 0 0 0 1 1 0.464025 0.000000 + 12 C4 CT 0 0 0 1 1 0.170032 0.000000 + 13 H4 H1 0 0 0 1 1 -0.033343 0.000000 + 14 O4 OH 0 0 0 1 1 -0.688254 0.000000 + 15 HO4 HO 0 0 0 1 1 0.325372 0.000000 + 16 C5 CT 0 0 0 1 1 0.633759 0.000000 + 17 H5 H1 0 0 0 1 1 0.006036 0.000000 + 18 C6 CT 4 0 0 1 1 -0.248292 0.000000 + 192H6 H1 0 0 0 1 1 0.101066 0.000000 + 203H6 H1 0 0 0 1 1 0.101066 0.000000 + 21 OR OS 0 0 0 1 1 -0.781085 0.000000 + 1 2 + 1 3 + 1 4 + 1 21 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 16 21 + 18 19 + 18 20 diff --git a/src/data/amber_q/lps_ec/GN1.frg b/src/data/amber_q/lps_ec/GN1.frg new file mode 100644 index 0000000..c7f3b57 --- /dev/null +++ b/src/data/amber_q/lps_ec/GN1.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 08:58:30 +# +$GN1 + 23 1 1 0 +GN1 + 1 C1 AC 3 0 0 1 1 0.113419 0.000000 + 2 H1 H2 0 0 0 1 1 0.072233 0.000000 + 3 C2 CT 0 0 0 1 1 -0.186703 0.000000 + 4 H2 H1 0 0 0 1 1 0.430869 0.000000 + 5 N N 0 1 0 1 1 -0.216291 0.000000 + 6 H H 0 0 0 1 1 0.150137 0.000000 + 7 C C 4 1 0 1 1 0.491961 0.000000 + 8 O O 0 0 0 1 1 -0.699036 0.000000 + 9 C3 CT 0 0 0 1 1 0.071114 0.000000 + 10 H3 H1 0 0 0 1 1 0.257830 0.000000 + 11 O3 OS 0 0 0 1 1 -0.660668 0.000000 + 12 C31 C 5 1 0 1 1 0.838466 0.000000 + 13 O31 O 0 0 0 1 1 -0.660802 0.000000 + 14 C4 CT 0 0 0 1 1 -.1417480 0.000000 + 15 H4 H1 0 0 0 1 1 0.358553 0.000000 + 16 O4 OH 0 0 0 1 1 -0.891694 0.000000 + 17 HO4 HO 0 0 0 1 1 0.512610 0.000000 + 18 C5 CT 0 0 0 1 1 0.490790 0.000000 + 19 H5 H1 0 0 0 1 1 0.000061 0.000000 + 20 C6 CT 6 0 0 1 1 0.194970 0.000000 + 212H6 H1 0 0 0 1 1 -0.034709 0.000000 + 223H6 H1 0 0 0 1 1 -0.034709 0.000000 + 23 OR OS 0 0 0 1 1 -0.456655 0.000000 + 1 2 + 1 3 + 1 23 + 3 4 + 3 5 + 3 9 + 5 6 + 5 7 + 7 8 + 9 10 + 9 11 + 9 14 + 11 12 + 12 13 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 23 + 20 21 + 20 22 diff --git a/src/data/amber_q/lps_ec/GN2.frg b/src/data/amber_q/lps_ec/GN2.frg new file mode 100644 index 0000000..7d5a454 --- /dev/null +++ b/src/data/amber_q/lps_ec/GN2.frg @@ -0,0 +1,53 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$GN2 + 22 1 1 0 +GN2 + 1 C1 AC 0 0 0 1 1 0.867086 0.000000 + 2 H1 H2 0 0 0 1 1 0.027072 0.000000 + 3 O1 OS 3 0 0 1 1 -0.352386 0.000000 + 4 C2 CT 0 0 0 1 1 0.087392 0.000000 + 5 H2 H1 0 0 0 1 1 0.644627 0.000000 + 6 N N 0 1 0 1 1 -0.482697 0.000000 + 7 H H 0 0 0 1 1 0.245772 0.000000 + 8 C C 4 1 0 1 1 0.842243 0.000000 + 9 O O 0 0 0 1 1 -0.644087 0.000000 + 10 C3 CT 0 0 0 1 1 -0.566141 0.000000 + 11 H3 H1 0 0 0 1 1 0.436671 0.000000 + 12 O3 OS 0 0 0 1 1 -0.576950 0.000000 + 13 CO3 C 5 1 0 1 1 0.821854 0.000000 + 14 OO3 O 0 0 0 1 1 -0.653878 0.000000 + 15 C4 CT 6 0 0 1 1 -0.437006 0.000000 + 16 H4 H1 0 0 0 1 1 0.057250 0.000000 + 17 C5 CT 0 0 0 1 1 1.056769 0.000000 + 18 H5 H1 0 0 0 1 1 -0.185588 0.000000 + 19 C6 CT 7 0 0 1 1 -0.579400 0.000000 + 202H6 H1 0 0 0 1 1 0.127390 0.000000 + 213H6 H1 0 0 0 1 1 0.127390 0.000000 + 22 OR OS 0 0 0 1 1 -0.863384 0.000000 + 1 2 + 1 3 + 1 4 + 1 22 + 4 5 + 4 6 + 4 10 + 6 7 + 6 8 + 8 9 + 10 11 + 10 12 + 10 15 + 12 13 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 22 + 19 20 + 19 21 diff --git a/src/data/amber_q/lps_ec/HE1.frg b/src/data/amber_q/lps_ec/HE1.frg new file mode 100644 index 0000000..47c53b7 --- /dev/null +++ b/src/data/amber_q/lps_ec/HE1.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE1 + 23 1 1 0 +HE1 + 1 C1 AC 0 0 0 1 1 0.592716 0.000000 + 2 H1 H2 0 0 0 1 1 0.127829 0.000000 + 3 O1 OS 3 0 0 1 1 -0.173746 0.000000 + 4 C2 CT 0 0 0 1 1 0.232872 0.000000 + 5 H2 H1 0 0 0 1 1 0.131111 0.000000 + 6 O2 OH 0 0 0 1 1 -0.641843 0.000000 + 7 HO2 HO 0 0 0 1 1 0.320002 0.000000 + 8 C3 CT 4 0 0 1 1 -0.228802 0.000000 + 9 H3 H1 0 0 0 1 1 0.132071 0.000000 + 10 C4 CT 5 0 0 1 1 -0.208550 0.000000 + 11 H4 H1 0 0 0 1 1 0.037906 0.000000 + 12 C5 CT 0 0 0 1 1 0.604080 0.000000 + 13 H5 H1 0 0 0 1 1 0.024648 0.000000 + 14 C6 CT 0 0 0 1 1 0.382943 0.000000 + 15 H6 H1 0 0 0 1 1 -0.005643 0.000000 + 16 O6 OH 0 0 0 1 1 -0.767993 0.000000 + 17 HO6 HO 0 0 0 1 1 0.474382 0.000000 + 18 C7 CT 0 0 0 1 1 0.192162 0.000000 + 192H7 H1 0 0 0 1 1 0.030341 0.000000 + 203H7 H1 0 0 0 1 1 0.030341 0.000000 + 21 O7 OH 0 0 0 1 1 -0.730966 0.000000 + 22 HO7 HO 0 0 0 1 1 0.397321 0.000000 + 23 OR OS 0 0 0 1 1 -0.953182 0.000000 + 1 2 + 1 3 + 1 4 + 1 23 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 10 11 + 10 12 + 12 13 + 12 14 + 12 23 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/lps_ec/HE2.frg b/src/data/amber_q/lps_ec/HE2.frg new file mode 100644 index 0000000..ea2906f --- /dev/null +++ b/src/data/amber_q/lps_ec/HE2.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE2 + 21 1 1 0 +HE2 + 1 C1 AC 0 0 0 1 1 0.055732 0.000000 + 2 H1 H2 0 0 0 1 1 0.297481 0.000000 + 3 O1 OS 3 0 0 1 1 -0.009603 0.000000 + 4 C2 CT 0 0 0 1 1 0.486124 0.000000 + 5 H2 H1 0 0 0 1 1 0.052431 0.000000 + 6 O2 OH 0 0 0 1 1 -1.072662 0.000000 + 7 HO2 HO 0 0 0 1 1 0.424104 0.000000 + 8 C3 CT 4 0 0 1 1 -0.150164 0.000000 + 9 H3 H1 0 0 0 1 1 0.107220 0.000000 + 10 C4 CT 5 0 0 1 1 -0.202032 0.000000 + 11 H4 H1 0 0 0 1 1 0.010899 0.000000 + 12 C5 CT 0 0 0 1 1 0.499131 0.000000 + 13 H5 H1 0 0 0 1 1 0.004472 0.000000 + 14 C6 CT 0 0 0 1 1 0.438346 0.000000 + 15 H6 H1 0 0 0 1 1 0.094474 0.000000 + 16 O6 OH 0 0 0 1 1 -0.956445 0.000000 + 17 HO6 HO 0 0 0 1 1 0.658432 0.000000 + 18 C7 CT 6 0 0 1 1 -0.313208 0.000000 + 192H7 H1 0 0 0 1 1 0.071185 0.000000 + 203H7 H1 0 0 0 1 1 0.071185 0.000000 + 21 OR OS 0 0 0 1 1 -0.567101 0.000000 + 1 2 + 1 3 + 1 4 + 1 21 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 10 11 + 10 12 + 12 13 + 12 14 + 12 21 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 diff --git a/src/data/amber_q/lps_ec/HE3.frg b/src/data/amber_q/lps_ec/HE3.frg new file mode 100644 index 0000000..88b156a --- /dev/null +++ b/src/data/amber_q/lps_ec/HE3.frg @@ -0,0 +1,63 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE3 + 27 1 1 0 +HE3 + 1 C1 AC 0 0 0 1 1 0.233788 0.000000 + 2 H1 H2 0 0 0 1 1 0.115911 0.000000 + 3 O1 OS 3 0 0 1 1 -0.065698 0.000000 + 4 C2 CT 0 0 0 1 1 0.293831 0.000000 + 5 H2 H1 0 0 0 1 1 0.096511 0.000000 + 6 O2 OH 0 0 0 1 1 -0.802055 0.000000 + 7 HO2 HO 0 0 0 1 1 0.423832 0.000000 + 8 C3 CT 0 0 0 1 1 0.529912 0.000000 + 9 H3 H1 0 0 0 1 1 0.093653 0.000000 + 10 O3 OH 0 0 0 1 1 -1.174772 0.000000 + 11 HO3 HO 0 0 0 1 1 0.552521 0.000000 + 12 C4 CT 0 0 0 1 1 0.394630 0.000000 + 13 H4 H1 0 0 0 1 1 0.096111 0.000000 + 14 O4 OH 0 0 0 1 1 -0.771900 0.000000 + 15 HO4 HO 0 0 0 1 1 0.416045 0.000000 + 16 C5 CT 0 0 0 1 1 0.137365 0.000000 + 17 H5 H1 0 0 0 1 1 -0.086477 0.000000 + 18 C6 CT 0 0 0 1 1 0.625346 0.000000 + 19 H6 H1 0 0 0 1 1 -0.050535 0.000000 + 20 O6 OH 0 0 0 1 1 -0.839967 0.000000 + 21 HO6 HO 0 0 0 1 1 0.458187 0.000000 + 22 C7 CT 0 0 0 1 1 0.264072 0.000000 + 232H7 H1 0 0 0 1 1 0.001987 0.000000 + 243H7 H1 0 0 0 1 1 0.001987 0.000000 + 25 O7 OH 0 0 0 1 1 -0.798300 0.000000 + 26 HO7 HO 0 0 0 1 1 0.466929 0.000000 + 27 OR OS 0 0 0 1 1 -0.612914 0.000000 + 1 2 + 1 3 + 1 4 + 1 27 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 16 27 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/lps_ec/HE4.frg b/src/data/amber_q/lps_ec/HE4.frg new file mode 100644 index 0000000..297681f --- /dev/null +++ b/src/data/amber_q/lps_ec/HE4.frg @@ -0,0 +1,63 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE4 + 27 1 1 0 +HE4 + 1 C1 AC 0 0 0 1 1 0.543249 0.000000 + 2 H1 H2 0 0 0 1 1 0.053887 0.000000 + 3 O1 OS 3 0 0 1 1 -0.289124 0.000000 + 4 C2 CT 0 0 0 1 1 0.207822 0.000000 + 5 H2 H1 0 0 0 1 1 0.074666 0.000000 + 6 O2 OH 0 0 0 1 1 -0.814166 0.000000 + 7 HO2 HO 0 0 0 1 1 0.490041 0.000000 + 8 C3 CT 0 0 0 1 1 0.578052 0.000000 + 9 H3 H1 0 0 0 1 1 -0.059410 0.000000 + 10 O3 OH 0 0 0 1 1 -0.827632 0.000000 + 11 HO3 HO 0 0 0 1 1 0.468295 0.000000 + 12 C4 CT 0 0 0 1 1 0.014820 0.000000 + 13 H4 H1 0 0 0 1 1 0.072476 0.000000 + 14 O4 OH 0 0 0 1 1 -0.741547 0.000000 + 15 HO4 HO 0 0 0 1 1 0.436432 0.000000 + 16 C5 CT 0 0 0 1 1 0.397046 0.000000 + 17 H5 H1 0 0 0 1 1 0.048543 0.000000 + 18 C6 CT 0 0 0 1 1 0.261450 0.000000 + 19 H6 H1 0 0 0 1 1 -0.001659 0.000000 + 20 O6 OH 0 0 0 1 1 -0.726431 0.000000 + 21 HO6 HO 0 0 0 1 1 0.435584 0.000000 + 22 C7 CT 0 0 0 1 1 0.323405 0.000000 + 232H7 H1 0 0 0 1 1 0.003574 0.000000 + 243H7 H1 0 0 0 1 1 0.003574 0.000000 + 25 O7 OH 0 0 0 1 1 -0.723675 0.000000 + 26 HO7 HO 0 0 0 1 1 0.449974 0.000000 + 27 OR OS 0 0 0 1 1 -0.679246 0.000000 + 1 2 + 1 3 + 1 4 + 1 27 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 16 27 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/lps_ec/KD1.frg b/src/data/amber_q/lps_ec/KD1.frg new file mode 100644 index 0000000..66707e5 --- /dev/null +++ b/src/data/amber_q/lps_ec/KD1.frg @@ -0,0 +1,57 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$KD1 + 24 1 1 0 +KD1 + 1 C1 C 0 1 0 1 1 1.609759 0.000000 + 2 O11 O2 0 0 0 1 1 -1.420645 0.000000 + 3 O12 O2 0 0 0 1 1 -1.095936 0.000000 + 4 C2 AC 0 0 0 1 1 0.316410 0.000000 + 5 O2 OS 3 0 0 1 1 -0.089481 0.000000 + 6 C3 CT 0 0 0 1 1 -0.039435 0.000000 + 72H3 HC 0 0 0 1 1 0.041299 0.000000 + 83H3 HC 0 0 0 1 1 0.041299 0.000000 + 9 C4 CT 4 0 0 1 1 -0.133820 0.000000 + 10 H4 H1 0 0 0 1 1 0.154209 0.000000 + 11 C5 CT 5 0 0 1 1 -0.306006 0.000000 + 12 H5 H1 0 0 0 1 1 0.234593 0.000000 + 13 C6 CT 0 0 0 1 1 0.294750 0.000000 + 14 H6 H1 0 0 0 1 1 0.034444 0.000000 + 15 C7 CT 0 0 0 1 1 0.090478 0.000000 + 16 H7 H1 0 0 0 1 1 0.091281 0.000000 + 17 O7 OH 0 0 0 1 1 -0.740663 0.000000 + 18 HO7 HO 0 0 0 1 1 0.425276 0.000000 + 19 C8 CT 0 0 0 1 1 0.648942 0.000000 + 202H8 H1 0 0 0 1 1 -0.110336 0.000000 + 213H8 H1 0 0 0 1 1 -0.110336 0.000000 + 22 O8 OH 0 0 0 1 1 -0.840923 0.000000 + 23 HO8 HO 0 0 0 1 1 0.462830 0.000000 + 24 OR OS 0 0 0 1 1 -0.557987 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 24 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 11 12 + 11 13 + 13 14 + 13 15 + 13 24 + 15 16 + 15 17 + 15 19 + 17 18 + 19 20 + 19 21 + 19 22 + 22 23 diff --git a/src/data/amber_q/lps_ec/KD2.frg b/src/data/amber_q/lps_ec/KD2.frg new file mode 100644 index 0000000..8c61822 --- /dev/null +++ b/src/data/amber_q/lps_ec/KD2.frg @@ -0,0 +1,65 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$KD2 + 28 1 1 0 +KD2 + 1 C1 C 0 1 0 1 1 1.194884 0.000000 + 2 O11 O2 0 0 0 1 1 -1.006920 0.000000 + 3 O12 O2 0 0 0 1 1 -1.032685 0.000000 + 4 C2 AC 0 0 0 1 1 0.247898 0.000000 + 5 O2 OS 3 0 0 1 1 -0.169823 0.000000 + 6 C3 CT 0 0 0 1 1 -0.112596 0.000000 + 72H3 HC 0 0 0 1 1 0.029839 0.000000 + 83H3 HC 0 0 0 1 1 0.029839 0.000000 + 9 C4 CT 0 0 0 1 1 0.398654 0.000000 + 10 H4 H1 0 0 0 1 1 -0.021858 0.000000 + 11 O4 OH 0 0 0 1 1 -0.812111 0.000000 + 12 HO4 HO 0 0 0 1 1 0.469651 0.000000 + 13 C5 CT 0 0 0 1 1 0.444025 0.000000 + 14 H5 H1 0 0 0 1 1 -0.039673 0.000000 + 15 O5 OH 0 0 0 1 1 -0.806948 0.000000 + 16 HO5 HO 0 0 0 1 1 0.460309 0.000000 + 17 C6 CT 0 0 0 1 1 0.214383 0.000000 + 18 H6 H1 0 0 0 1 1 0.052915 0.000000 + 19 C7 CT 0 0 0 1 1 0.404323 0.000000 + 20 H7 H1 0 0 0 1 1 0.015334 0.000000 + 21 O7 OH 0 0 0 1 1 -0.891275 0.000000 + 22 HO7 HO 0 0 0 1 1 0.507523 0.000000 + 23 C8 CT 0 0 0 1 1 0.152401 0.000000 + 242H8 H1 0 0 0 1 1 0.030152 0.000000 + 253H8 H1 0 0 0 1 1 0.030152 0.000000 + 26 O8 OH 0 0 0 1 1 -0.701123 0.000000 + 27 HO8 HO 0 0 0 1 1 0.451598 0.000000 + 28 OR OS 0 0 0 1 1 -0.538866 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 28 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 13 + 11 12 + 13 14 + 13 15 + 13 17 + 15 16 + 17 18 + 17 19 + 17 28 + 19 20 + 19 21 + 19 23 + 21 22 + 23 24 + 23 25 + 23 26 + 26 27 diff --git a/src/data/amber_q/lps_ec/PO4.frg b/src/data/amber_q/lps_ec/PO4.frg new file mode 100644 index 0000000..e364974 --- /dev/null +++ b/src/data/amber_q/lps_ec/PO4.frg @@ -0,0 +1,18 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$PO4 + 5 1 1 0 +PO4 + 1 OP1 OS 3 0 0 1 1 -0.139474 0.000000 + 2 P P 0 0 0 1 1 0.938933 0.000000 + 3 OP2 O2 0 0 0 1 1 -0.933153 0.000000 + 4 OP3 O2 0 0 0 1 1 -0.933153 0.000000 + 5 OP4 O2 0 0 0 1 1 -0.933153 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 diff --git a/src/data/amber_q/lps_ec/POC.frg b/src/data/amber_q/lps_ec/POC.frg new file mode 100644 index 0000000..71e9a5c --- /dev/null +++ b/src/data/amber_q/lps_ec/POC.frg @@ -0,0 +1,35 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude estimates +# 08/24/05 11:36:33 +# +$POC + 14 1 1 0 +POC + 1 C1 CT 3 0 0 1 1 -0.104211 0.000000 + 22H1 HC 0 0 0 1 1 0.010288 0.000000 + 33H1 HC 0 0 0 1 1 0.010288 0.000000 + 4 C2 CT 0 0 0 1 1 0.330088 0.000000 + 5 H2 H1 0 0 0 1 1 -0.000292 0.000000 + 6 O2 OS 0 0 0 1 1 -0.633243 0.000000 + 7 C3 CT 4 0 0 1 1 0.016752 0.000000 + 82H3 HC 0 0 0 1 1 0.001054 0.000000 + 93H3 HC 0 0 0 1 1 0.001054 0.000000 + 10 C4 C 0 1 0 1 1 0.782302 0.000000 + 11 O4 O 0 0 0 1 1 -0.540273 0.000000 + 12 C5 CT 5 0 0 1 1 -0.017987 0.000000 + 132H5 HC 0 0 0 1 1 0.072090 0.000000 + 143H5 HC 0 0 0 1 1 0.072090 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 6 10 + 7 8 + 7 9 + 10 11 + 10 12 + 12 13 + 12 14 diff --git a/src/data/amber_q/lps_ec/POH.frg b/src/data/amber_q/lps_ec/POH.frg new file mode 100644 index 0000000..dbdd0f0 --- /dev/null +++ b/src/data/amber_q/lps_ec/POH.frg @@ -0,0 +1,28 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$POH + 10 1 1 0 +POH + 1 C1 CT 3 0 0 1 1 0.341188 0.000000 + 22H1 HC 0 0 0 1 1 -0.101849 0.000000 + 33H1 HC 0 0 0 1 1 -0.101849 0.000000 + 4 C2 CT 0 0 0 1 1 0.432090 0.000000 + 5 H2 H1 0 0 0 1 1 0.030800 0.000000 + 6 O2 OH 0 0 0 1 1 -0.860879 0.000000 + 7 HO2 HO 0 0 0 1 1 0.450697 0.000000 + 8 C3 CT 4 0 0 1 1 -0.583445 0.000000 + 92H3 HC 0 0 0 1 1 0.196624 0.000000 + 103H3 HC 0 0 0 1 1 0.196624 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 diff --git a/src/data/amber_q/lps_ec/PT1.frg b/src/data/amber_q/lps_ec/PT1.frg new file mode 100644 index 0000000..b2db1a7 --- /dev/null +++ b/src/data/amber_q/lps_ec/PT1.frg @@ -0,0 +1,40 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$PT1 + 16 1 1 0 +PT1 + 1 C1 CT 3 0 0 1 1 0.195684 0.000000 + 22H1 HC 0 0 0 1 1 -0.062894 0.000000 + 33H1 HC 0 0 0 1 1 -0.062894 0.000000 + 4 C2 CT 0 0 0 1 1 0.011013 0.000000 + 52H2 HC 0 0 0 1 1 0.029913 0.000000 + 63H2 HC 0 0 0 1 1 0.029913 0.000000 + 7 C3 CT 0 0 0 1 1 -0.682627 0.000000 + 82H3 HC 0 0 0 1 1 0.218569 0.000000 + 93H3 HC 0 0 0 1 1 0.218569 0.000000 + 10 C4 CT 0 0 0 1 1 0.107450 0.000000 + 112H4 HC 0 0 0 1 1 0.035748 0.000000 + 123H4 HC 0 0 0 1 1 0.035748 0.000000 + 13 C5 CT 0 0 0 1 1 -0.030578 0.000000 + 142H5 HC 0 0 0 1 1 -0.014538 0.000000 + 153H5 HC 0 0 0 1 1 -0.014538 0.000000 + 164H5 HC 0 0 0 1 1 -0.014538 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 diff --git a/src/data/amber_q/lps_ec/PT2.frg b/src/data/amber_q/lps_ec/PT2.frg new file mode 100644 index 0000000..f97d6c3 --- /dev/null +++ b/src/data/amber_q/lps_ec/PT2.frg @@ -0,0 +1,38 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$PT2 + 15 1 1 0 +PT2 + 1 C1 CT 3 0 0 1 1 -0.241902 0.000000 + 22H1 HC 0 0 0 1 1 0.025797 0.000000 + 33H1 HC 0 0 0 1 1 0.025797 0.000000 + 4 C2 CT 0 0 0 1 1 0.484331 0.000000 + 52H2 HC 0 0 0 1 1 -0.132786 0.000000 + 63H2 HC 0 0 0 1 1 -0.132786 0.000000 + 7 C3 CT 0 0 0 1 1 0.606360 0.000000 + 82H3 HC 0 0 0 1 1 -0.018041 0.000000 + 93H3 HC 0 0 0 1 1 -0.018041 0.000000 + 10 C4 CT 0 0 0 1 1 -0.077118 0.000000 + 112H4 HC 0 0 0 1 1 0.047634 0.000000 + 123H4 HC 0 0 0 1 1 0.047634 0.000000 + 13 C5 CT 4 0 0 1 1 -0.095495 0.000000 + 142H5 HC 0 0 0 1 1 0.012170 0.000000 + 153H5 HC 0 0 0 1 1 0.012170 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 diff --git a/src/data/amber_s/ACE.frg b/src/data/amber_s/ACE.frg new file mode 100644 index 0000000..631b118 --- /dev/null +++ b/src/data/amber_s/ACE.frg @@ -0,0 +1,14 @@ +$ACE + 6 1 1 0 +ACE + 12HH3 HC 0 0 0 1 1 0.112300 0.000000 + 2 CH3 CT 0 0 0 1 1 -0.366200 0.000000 + 33HH3 HC 0 0 0 1 1 0.112300 0.000000 + 44HH3 HC 0 0 0 1 1 0.112300 0.000000 + 5 C C 2 1 0 1 1 0.597200 0.000000 + 6 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 + 3 2 + 4 2 + 5 2 + 6 5 diff --git a/src/data/amber_s/ACE_N.sgm b/src/data/amber_s/ACE_N.sgm new file mode 100644 index 0000000..2b30a4b --- /dev/null +++ b/src/data/amber_s/ACE_N.sgm @@ -0,0 +1,47 @@ +# +$ACE_N + 4.600000 + 6 5 7 3 0 0 1 1 + 0.000000 + 1 CH3 0 0 0 1 1 + CT -0.366200 0.000000 + 22HH3 0 0 0 1 1 + HC 0.112300 0.000000 + 33HH3 0 0 0 1 1 + HC 0.112300 0.000000 + 44HH3 0 0 0 1 1 + HC 0.112300 0.000000 + 5 C 2 1 0 1 1 + C 0.597200 0.000000 + 6 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 5 6 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 2 1 5 0 0 + 0.000000 0.00000E+00 + 4 3 1 4 0 0 + 0.000000 0.00000E+00 + 5 3 1 5 0 0 + 0.000000 0.00000E+00 + 6 4 1 5 0 0 + 0.000000 0.00000E+00 + 7 1 5 6 0 0 + 0.000000 0.00000E+00 + 1 2 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 2 3 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 3 4 1 5 6 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/ALA.frg b/src/data/amber_s/ALA.frg new file mode 100644 index 0000000..effc66e --- /dev/null +++ b/src/data/amber_s/ALA.frg @@ -0,0 +1,16 @@ +$ALA + 10 1 1 0 +ALA + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 0.033700 0.000000 + 4 HA H1 0 0 0 1 1 0.082300 0.000000 + 5 CB CT 0 0 0 1 1 -0.182500 0.000000 + 62HB HC 0 0 0 1 1 0.060300 0.000000 + 73HB HC 0 0 0 1 1 0.060300 0.000000 + 84HB HC 0 0 0 1 1 0.060300 0.000000 + 9 C C 2 1 0 1 1 0.597300 0.000000 + 10 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 3 9 10 + 4 3 5 6 + 7 5 8 diff --git a/src/data/amber_s/ALA.sgm b/src/data/amber_s/ALA.sgm new file mode 100644 index 0000000..2a8abe7 --- /dev/null +++ b/src/data/amber_s/ALA.sgm @@ -0,0 +1,102 @@ +# +$ALA + 4.600000 + 10 9 14 15 0 1 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT 0.033700 0.000000 + 4 HA 0 0 0 1 1 + H1 0.082300 0.000000 + 5 CB 0 0 0 1 1 + CT -0.182500 0.000000 + 62HB 0 0 0 1 1 + HC 0.060300 0.000000 + 73HB 0 0 0 1 1 + HC 0.060300 0.000000 + 84HB 0 0 0 1 1 + HC 0.060300 0.000000 + 9 C 2 1 0 1 1 + C 0.597300 0.000000 + 10 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 9 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 9 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 9 0 0 + 0.000000 0.00000E+00 + 7 5 3 9 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 3 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 9 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 9 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 9 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 9 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 1 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 14 4 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 15 5 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 1 5 3 9 1 0.152500 diff --git a/src/data/amber_s/ALA_C.frg b/src/data/amber_s/ALA_C.frg new file mode 100644 index 0000000..806401c --- /dev/null +++ b/src/data/amber_s/ALA_C.frg @@ -0,0 +1,24 @@ +$ALA_C + 11 1 1 0 +ALA_C + 1 N N 1 1 0 1 1 -0.382100 0.000000 + 2 H H 0 0 0 1 1 0.268100 0.000000 + 3 CA CT 0 0 0 1 1 -0.174700 0.000000 + 4 HA H1 0 0 0 1 1 0.106700 0.000000 + 5 CB CT 0 0 0 1 1 -0.209300 0.000000 + 62HB HC 0 0 0 1 1 0.076400 0.000000 + 73HB HC 0 0 0 1 1 0.076400 0.000000 + 84HB HC 0 0 0 1 1 0.076400 0.000000 + 9 C C 0 1 0 1 1 0.773100 0.000000 + 10 O O2 0 0 0 1 1 -0.805500 0.000000 + 11 OXT O2 0 0 0 1 1 -0.805500 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 5 + 7 5 + 8 5 + 9 3 + 10 9 + 11 9 diff --git a/src/data/amber_s/ALA_C.sgm b/src/data/amber_s/ALA_C.sgm new file mode 100644 index 0000000..3cadd5d --- /dev/null +++ b/src/data/amber_s/ALA_C.sgm @@ -0,0 +1,117 @@ +# +$ALA_C + 4.600000 + 11 10 16 18 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.382100 0.000000 + 2 H 0 0 0 1 1 + H 0.268100 0.000000 + 3 CA 0 0 0 1 1 + CT -0.174700 0.000000 + 4 HA 0 0 0 1 1 + H1 0.106700 0.000000 + 5 CB 0 0 0 1 1 + CT -0.209300 0.000000 + 62HB 0 0 0 1 1 + HC 0.076400 0.000000 + 73HB 0 0 0 1 1 + HC 0.076400 0.000000 + 84HB 0 0 0 1 1 + HC 0.076400 0.000000 + 9 C 0 1 0 1 1 + C 0.773100 0.000000 + 10 O 0 0 0 1 1 + O2 -0.805500 0.000000 + 11 OXT 0 0 0 1 1 + O2 -0.805500 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 9 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 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+ 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 9 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 9 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 9 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 4 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 14 1 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 15 1 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 17 5 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 18 5 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 1 3 10 9 11 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/ALA_N.frg b/src/data/amber_s/ALA_N.frg new file mode 100644 index 0000000..73ce033 --- /dev/null +++ b/src/data/amber_s/ALA_N.frg @@ -0,0 +1,26 @@ +$ALA_N + 12 1 1 0 +ALA_N + 1 N N3 0 0 0 1 1 0.141400 0.000000 + 22H H 0 0 0 1 1 0.199700 0.000000 + 33H H 0 0 0 1 1 0.199700 0.000000 + 44H H 0 0 0 1 1 0.199700 0.000000 + 5 CA CT 0 0 0 1 1 0.096200 0.000000 + 6 HA HP 0 0 0 1 1 0.088900 0.000000 + 7 CB CT 0 0 0 1 1 -0.059700 0.000000 + 82HB HC 0 0 0 1 1 0.030000 0.000000 + 93HB 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0.00000E+00 + 1 5 9 8 10 0 0 + 0 0.000000 0.00000E+00 + 2 3 12 11 13 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/ASP_N.frg b/src/data/amber_s/ASP_N.frg new file mode 100644 index 0000000..35873d5 --- /dev/null +++ b/src/data/amber_s/ASP_N.frg @@ -0,0 +1,30 @@ +$ASP_N + 14 1 1 0 +ASP_N + 1 N N3 0 0 0 1 1 0.078200 0.000000 + 22H H 0 0 0 1 1 0.220000 0.000000 + 33H H 0 0 0 1 1 0.220000 0.000000 + 44H H 0 0 0 1 1 0.220000 0.000000 + 5 CA CT 0 0 0 1 1 0.029200 0.000000 + 6 HA HP 0 0 0 1 1 0.114100 0.000000 + 7 CB CT 0 0 0 1 1 -0.023500 0.000000 + 82HB HC 0 0 0 1 1 -0.016900 0.000000 + 93HB HC 0 0 0 1 1 -0.016900 0.000000 + 10 CG C 0 1 0 1 1 0.819400 0.000000 + 11 OD1 O2 0 0 0 1 1 -0.808400 0.000000 + 12 OD2 O2 0 0 0 1 1 -0.808400 0.000000 + 13 C C 2 1 0 1 1 0.562100 0.000000 + 14 O O 0 0 0 1 1 -0.588900 0.000000 + 2 1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 7 + 11 10 + 12 10 + 13 5 + 14 13 diff --git a/src/data/amber_s/ASP_N.sgm b/src/data/amber_s/ASP_N.sgm new file 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0000000..4dca8a4 --- /dev/null +++ b/src/data/amber_s/CYS_C.frg @@ -0,0 +1,19 @@ +$CYS_C + 12 1 1 0 +CYS_C + 1 N N 1 1 0 1 1 -0.382100 0.000000 + 2 H H 0 0 0 1 1 0.268100 0.000000 + 3 CA CT 0 0 0 1 1 -0.163500 0.000000 + 4 HA H1 0 0 0 1 1 0.139600 0.000000 + 5 CB CT 0 0 0 1 1 -0.199600 0.000000 + 62HB H1 0 0 0 1 1 0.143700 0.000000 + 73HB H1 0 0 0 1 1 0.143700 0.000000 + 8 SG SH 0 0 0 1 1 -0.310200 0.000000 + 9 HSG HS 0 0 0 1 1 0.206800 0.000000 + 10 C C 0 1 0 1 1 0.749700 0.000000 + 11 O O2 0 0 0 1 1 -0.798100 0.000000 + 12 OXT O2 0 0 0 1 1 -0.798100 0.000000 + 2 1 3 10 11 + 10 12 + 4 3 5 8 9 + 6 5 7 diff --git a/src/data/amber_s/CYS_C.sgm b/src/data/amber_s/CYS_C.sgm new file mode 100644 index 0000000..a10e650 --- /dev/null +++ b/src/data/amber_s/CYS_C.sgm @@ -0,0 +1,129 @@ +# +$CYS_C + 4.600000 + 12 11 17 21 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.382100 0.000000 + 2 H 0 0 0 1 1 + H 0.268100 0.000000 + 3 CA 0 0 0 1 1 + CT -0.163500 0.000000 + 4 HA 0 0 0 1 1 + H1 0.139600 0.000000 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1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 7 + 11 10 + 12 5 + 13 12 diff --git a/src/data/amber_s/CYS_N.sgm b/src/data/amber_s/CYS_N.sgm new file mode 100644 index 0000000..468fc0a --- /dev/null +++ b/src/data/amber_s/CYS_N.sgm @@ -0,0 +1,143 @@ +# +$CYS_N + 4.600000 + 13 12 20 24 0 0 1 1 + 0.000000 + 1 N 0 0 0 1 1 + N3 0.132500 0.000000 + 22H 0 0 0 1 1 + H 0.202300 0.000000 + 33H 0 0 0 1 1 + H 0.202300 0.000000 + 44H 0 0 0 1 1 + H 0.202300 0.000000 + 5 CA 0 0 0 1 1 + CT 0.092700 0.000000 + 6 HA 0 0 0 1 1 + HP 0.141100 0.000000 + 7 CB 0 0 0 1 1 + CT -0.119500 0.000000 + 82HB 0 0 0 1 1 + H1 0.118800 0.000000 + 93HB 0 0 0 1 1 + H1 0.118800 0.000000 + 10 SG 0 0 0 1 1 + SH -0.329800 0.000000 + 11 HG 0 0 0 1 1 + HS 0.197500 0.000000 + 12 C 2 1 0 1 1 + C 0.612300 0.000000 + 13 O 0 0 0 1 1 + O -0.571300 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 5 6 0 0 + 0.000000 0.00000E+00 + 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0.00000E+00 + 1 2 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 5 7 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 5 12 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 5 12 0 0 + 0 0.000000 0.00000E+00 + 7 4 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 1 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 1 5 12 0 0 + 0 0.000000 0.00000E+00 + 10 1 5 7 8 0 0 + 0 0.000000 0.00000E+00 + 11 1 5 7 9 0 0 + 0 0.000000 0.00000E+00 + 12 1 5 7 10 0 0 + 0 0.000000 0.00000E+00 + 13 6 5 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 6 5 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 6 5 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 12 5 7 8 0 0 + 0 0.000000 0.00000E+00 + 17 12 5 7 9 0 0 + 0 0.000000 0.00000E+00 + 18 12 5 7 10 0 0 + 0 0.000000 0.00000E+00 + 19 1 5 12 13 0 0 + 0 0.000000 0.00000E+00 + 20 6 5 12 13 0 0 + 0 0.000000 0.00000E+00 + 21 7 5 12 13 0 0 + 0 0.000000 0.00000E+00 + 22 5 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 24 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/CYX.frg b/src/data/amber_s/CYX.frg new file mode 100644 index 0000000..a16d5f1 --- /dev/null +++ b/src/data/amber_s/CYX.frg @@ -0,0 +1,22 @@ +$CYX + 10 1 1 0 +CYX + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 0.042900 0.000000 + 4 HA H1 0 0 0 1 1 0.076600 0.000000 + 5 CB CT 0 0 0 1 1 -0.079000 0.000000 + 62HB H1 0 0 0 1 1 0.091000 0.000000 + 73HB H1 0 0 0 1 1 0.091000 0.000000 + 8 SG S 3 0 0 1 1 -0.108100 0.000000 + 9 C C 2 1 0 1 1 0.597300 0.000000 + 10 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 5 + 7 5 + 8 5 + 9 3 + 10 9 diff --git a/src/data/amber_s/CYX.sgm b/src/data/amber_s/CYX.sgm new file mode 100644 index 0000000..43544e4 --- /dev/null +++ b/src/data/amber_s/CYX.sgm @@ -0,0 +1,101 @@ +# +$CYX + 4.600000 + 10 9 14 15 0 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT 0.042900 0.000000 + 4 HA 0 0 0 1 1 + H1 0.076600 0.000000 + 5 CB 0 0 0 1 1 + CT -0.079000 0.000000 + 62HB 0 0 0 1 1 + H1 0.091000 0.000000 + 73HB 0 0 0 1 1 + H1 0.091000 0.000000 + 8 SG 3 0 0 1 1 + S -0.108100 0.000000 + 9 C 2 1 0 1 1 + C 0.597300 0.000000 + 10 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 9 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 9 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 9 0 0 + 0.000000 0.00000E+00 + 7 5 3 9 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 3 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 9 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 9 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 9 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 9 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 1 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 14 4 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 15 5 3 9 10 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/CYX1.sgm b/src/data/amber_s/CYX1.sgm new file mode 100644 index 0000000..37677f5 --- /dev/null +++ b/src/data/amber_s/CYX1.sgm @@ -0,0 +1,107 @@ +# +$CYX1 + 4.600000 + 10 9 14 18 0 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT 0.042900 0.000000 + 4 HA 0 0 0 1 1 + H1 0.076600 0.000000 + 5 CB 0 0 0 1 1 + CT -0.079000 0.000000 + 62HB 0 0 0 1 1 + H1 0.091000 0.000000 + 73HB 0 0 0 1 1 + H1 0.091000 0.000000 + 8 SG 3 0 0 1 1 + S -0.108100 0.000000 + 9 C 2 1 0 1 1 + C 0.597300 0.000000 + 10 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 9 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 9 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 9 0 0 + 0.000000 0.00000E+00 + 7 5 3 9 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 3 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 9 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 9 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 9 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 9 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 4 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 14 1 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 15 1 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 17 5 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 18 5 3 9 11 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/CYX2.sgm b/src/data/amber_s/CYX2.sgm new file mode 100644 index 0000000..e48eac9 --- /dev/null +++ b/src/data/amber_s/CYX2.sgm @@ -0,0 +1,101 @@ +# +$CYX2 + 4.600000 + 10 9 14 15 0 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT 0.042900 0.000000 + 4 HA 0 0 0 1 1 + H1 0.076600 0.000000 + 5 CB 0 0 0 1 1 + CT -0.079000 0.000000 + 62HB 0 0 0 1 1 + H1 0.091000 0.000000 + 73HB 0 0 0 1 1 + H1 0.091000 0.000000 + 8 SG 3 0 0 1 1 + S -0.108100 0.000000 + 9 C 2 1 0 1 1 + C 0.597300 0.000000 + 10 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 9 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 9 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 9 0 0 + 0.000000 0.00000E+00 + 7 5 3 9 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 3 9 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 9 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 9 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 9 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 9 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 1 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 14 4 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 15 5 3 9 10 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/CYX_C.frg b/src/data/amber_s/CYX_C.frg new file mode 100644 index 0000000..00f973d --- /dev/null +++ b/src/data/amber_s/CYX_C.frg @@ -0,0 +1,24 @@ +$CYX_C + 11 1 1 0 +CYX_C + 1 N N 1 1 0 1 1 -0.382100 0.000000 + 2 H H 0 0 0 1 1 0.268100 0.000000 + 3 CA CT 0 0 0 1 1 -0.131800 0.000000 + 4 HA H1 0 0 0 1 1 0.093800 0.000000 + 5 CB CT 0 0 0 1 1 -0.194300 0.000000 + 62HB H1 0 0 0 1 1 0.122800 0.000000 + 73HB H1 0 0 0 1 1 0.122800 0.000000 + 8 SG S 3 0 0 1 1 -0.052900 0.000000 + 9 C C 0 1 0 1 1 0.761800 0.000000 + 10 O O2 0 0 0 1 1 -0.804100 0.000000 + 11 OXT O2 0 0 0 1 1 -0.804100 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 5 + 7 5 + 8 5 + 9 3 + 10 9 + 11 9 diff --git a/src/data/amber_s/CYX_C.sgm b/src/data/amber_s/CYX_C.sgm new file mode 100644 index 0000000..8674d65 --- /dev/null +++ b/src/data/amber_s/CYX_C.sgm @@ -0,0 +1,117 @@ +# +$CYX_C + 4.600000 + 11 10 16 18 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.382100 0.000000 + 2 H 0 0 0 1 1 + H 0.268100 0.000000 + 3 CA 0 0 0 1 1 + CT -0.131800 0.000000 + 4 HA 0 0 0 1 1 + H1 0.093800 0.000000 + 5 CB 0 0 0 1 1 + CT -0.194300 0.000000 + 62HB 0 0 0 1 1 + H1 0.122800 0.000000 + 73HB 0 0 0 1 1 + H1 0.122800 0.000000 + 8 SG 3 0 0 1 1 + S -0.052900 0.000000 + 9 C 0 1 0 1 1 + C 0.761800 0.000000 + 10 O 0 0 0 1 1 + O2 -0.804100 0.000000 + 11 OXT 0 0 0 1 1 + O2 -0.804100 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 9 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 9 10 0 0 + 0.000000 0.00000E+00 + 10 9 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 9 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 9 0 0 + 0.000000 0.00000E+00 + 7 5 3 9 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 3 9 10 0 0 + 0.000000 0.00000E+00 + 15 3 9 11 0 0 + 0.000000 0.00000E+00 + 16 10 9 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 9 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 9 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 9 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 9 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 4 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 14 1 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 15 1 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 16 4 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 17 5 3 9 10 0 0 + 0 0.000000 0.00000E+00 + 18 5 3 9 11 0 0 + 0 0.000000 0.00000E+00 + 1 3 10 9 11 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/CYX_N.frg b/src/data/amber_s/CYX_N.frg new file mode 100644 index 0000000..bb5d7c6 --- /dev/null +++ b/src/data/amber_s/CYX_N.frg @@ -0,0 +1,26 @@ +$CYX_N + 12 1 1 0 +CYX_N + 1 N N3 0 0 0 1 1 0.206900 0.000000 + 22H H 0 0 0 1 1 0.181500 0.000000 + 33H H 0 0 0 1 1 0.181500 0.000000 + 44H H 0 0 0 1 1 0.181500 0.000000 + 5 CA CT 0 0 0 1 1 0.105500 0.000000 + 6 HA HP 0 0 0 1 1 0.092200 0.000000 + 7 CB CT 0 0 0 1 1 -0.027700 0.000000 + 82HB H1 0 0 0 1 1 0.068000 0.000000 + 93HB H1 0 0 0 1 1 0.068000 0.000000 + 10 SG S 3 0 0 1 1 -0.098400 0.000000 + 11 C C 2 1 0 1 1 0.612300 0.000000 + 12 O O 0 0 0 1 1 -0.571300 0.000000 + 2 1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 7 + 11 5 + 12 11 diff --git a/src/data/amber_s/Cl.frg b/src/data/amber_s/Cl.frg new file mode 100644 index 0000000..b646282 --- /dev/null +++ b/src/data/amber_s/Cl.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$Cl_M + 1 1 1 0 +Cl_M + 1Cl Cl 0 0 0 1 1 -1.000000 0.000000 diff --git a/src/data/amber_s/Cl.sgm b/src/data/amber_s/Cl.sgm new file mode 100644 index 0000000..aee2d26 --- /dev/null +++ b/src/data/amber_s/Cl.sgm @@ -0,0 +1,7 @@ +# This is an automatically generated segment file +# + 4.600000 + 1 0 0 0 0 0 1 1 + 0.000000 + 1Cl 0 0 0 1 1 + Cl -1.000000 0.000000 diff --git a/src/data/amber_s/DA.frg b/src/data/amber_s/DA.frg new file mode 100644 index 0000000..247ea9f --- /dev/null +++ b/src/data/amber_s/DA.frg @@ -0,0 +1,70 @@ +#D-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group +$DA + 32 1 1 0 +D-ADEN + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 0.043100 0.000000 + 12 H1* H2 0 0 0 1 1 0.183800 0.000000 + 13 N9 N* 0 1 0 1 1 -0.026800 0.000000 + 14 C8 CK 0 1 0 1 1 0.160700 0.000000 + 15 H8 H5 0 0 0 1 1 0.187700 0.000000 + 16 N7 NB 0 0 0 1 1 -0.617500 0.000000 + 17 C5 CB 0 0 0 1 1 0.072500 0.000000 + 18 C6 CA 0 1 0 1 1 0.689700 0.000000 + 19 N6 N2 0 1 0 1 1 -0.912300 0.000000 + 202H6 H 0 0 0 1 1 0.416700 0.000000 + 213H6 H 0 0 0 1 1 0.416700 0.000000 + 22 N1 NC 0 0 0 1 1 -0.762400 0.000000 + 23 C2 CQ 0 1 0 1 1 0.571600 0.000000 + 24 H2 H5 0 0 0 1 1 0.059800 0.000000 + 25 N3 NC 0 0 0 1 1 -0.741700 0.000000 + 26 C4 CB 0 0 0 1 1 0.380000 0.000000 + 27 C3* CT 0 0 0 1 1 0.071300 0.000000 + 28 H3* H1 0 0 0 1 1 0.098500 0.000000 + 29 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 302H2* HC 0 0 0 1 1 0.071800 0.000000 + 313H2* HC 0 0 0 1 1 0.071800 0.000000 + 32 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 23 25 + 25 26 + 8 27 + 27 28 + 27 29 + 29 30 + 29 31 + 27 32 + 11 29 + 17 26 + 13 26 diff --git a/src/data/amber_s/DA_3.frg b/src/data/amber_s/DA_3.frg new file mode 100644 index 0000000..0fc7efc --- /dev/null +++ b/src/data/amber_s/DA_3.frg @@ -0,0 +1,72 @@ +#D-ADENOSINE - with 5' - phosphate group and 3' - OH group +$DA3 + 33 1 1 0 +D-ADEN + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 0.043100 0.000000 + 12 H1* H2 0 0 0 1 1 0.183800 0.000000 + 13 N9 N* 0 1 0 1 1 -0.026800 0.000000 + 14 C8 CK 0 1 0 1 1 0.160700 0.000000 + 15 H8 H5 0 0 0 1 1 0.187700 0.000000 + 16 N7 NB 0 0 0 1 1 -0.617500 0.000000 + 17 C5 CB 0 0 0 1 1 0.072500 0.000000 + 18 C6 CA 0 1 0 1 1 0.689700 0.000000 + 19 N6 N2 0 1 0 1 1 -0.912300 0.000000 + 202H6 H 0 0 0 1 1 0.416700 0.000000 + 213H6 H 0 0 0 1 1 0.416700 0.000000 + 22 N1 NC 0 0 0 1 1 -0.762400 0.000000 + 23 C2 CQ 0 1 0 1 1 0.571600 0.000000 + 24 H2 H5 0 0 0 1 1 0.059800 0.000000 + 25 N3 NC 0 0 0 1 1 -0.741700 0.000000 + 26 C4 CB 0 0 0 1 1 0.380000 0.000000 + 27 C3* CT 0 0 0 1 1 0.071300 0.000000 + 28 H3* H1 0 0 0 1 1 0.098500 0.000000 + 29 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 302H2* HC 0 0 0 1 1 0.071800 0.000000 + 313H2* HC 0 0 0 1 1 0.071800 0.000000 + 32 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 33 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 23 25 + 25 26 + 8 27 + 27 28 + 27 29 + 29 30 + 29 31 + 27 32 + 32 33 + 11 29 + 17 26 + 13 26 diff --git a/src/data/amber_s/DA_5.frg b/src/data/amber_s/DA_5.frg new file mode 100644 index 0000000..0a8396f --- /dev/null +++ b/src/data/amber_s/DA_5.frg @@ -0,0 +1,66 @@ +#D-ADENOSINE - with 5' - OH end group and 3' - O(minus) +$DA5 + 30 1 1 0 +D-ADEN + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 0.043100 0.000000 + 10 H1* H2 0 0 0 1 1 0.183800 0.000000 + 11 N9 N* 0 1 0 1 1 -0.026800 0.000000 + 12 C8 CK 0 1 0 1 1 0.160700 0.000000 + 13 H8 H5 0 0 0 1 1 0.187700 0.000000 + 14 N7 NB 0 0 0 1 1 -0.617500 0.000000 + 15 C5 CB 0 0 0 1 1 0.072500 0.000000 + 16 C6 CA 0 1 0 1 1 0.689700 0.000000 + 17 N6 N2 0 1 0 1 1 -0.912300 0.000000 + 182H6 H 0 0 0 1 1 0.416700 0.000000 + 193H6 H 0 0 0 1 1 0.416700 0.000000 + 20 N1 NC 0 0 0 1 1 -0.762400 0.000000 + 21 C2 CQ 0 1 0 1 1 0.571600 0.000000 + 22 H2 H5 0 0 0 1 1 0.059800 0.000000 + 23 N3 NC 0 0 0 1 1 -0.741700 0.000000 + 24 C4 CB 0 0 0 1 1 0.380000 0.000000 + 25 C3* CT 0 0 0 1 1 0.071300 0.000000 + 26 H3* H1 0 0 0 1 1 0.098500 0.000000 + 27 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 282H2* HC 0 0 0 1 1 0.071800 0.000000 + 293H2* HC 0 0 0 1 1 0.071800 0.000000 + 30 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 21 23 + 23 24 + 6 25 + 25 26 + 25 27 + 27 28 + 27 29 + 25 30 + 9 27 + 15 24 + 11 24 diff --git a/src/data/amber_s/DA_M.frg b/src/data/amber_s/DA_M.frg new file mode 100644 index 0000000..ce1d325 --- /dev/null +++ b/src/data/amber_s/DA_M.frg @@ -0,0 +1,68 @@ +#D-ADENOSINE - with 5' - OH group and 3' - OH group +$DAN + 31 1 1 0 +D-ADEN + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 0.043100 0.000000 + 10 H1* H2 0 0 0 1 1 0.183800 0.000000 + 11 N9 N* 0 1 0 1 1 -0.026800 0.000000 + 12 C8 CK 0 1 0 1 1 0.160700 0.000000 + 13 H8 H5 0 0 0 1 1 0.187700 0.000000 + 14 N7 NB 0 0 0 1 1 -0.617500 0.000000 + 15 C5 CB 0 0 0 1 1 0.072500 0.000000 + 16 C6 CA 0 1 0 1 1 0.689700 0.000000 + 17 N6 N2 0 1 0 1 1 -0.912300 0.000000 + 182H6 H 0 0 0 1 1 0.416700 0.000000 + 193H6 H 0 0 0 1 1 0.416700 0.000000 + 20 N1 NC 0 0 0 1 1 -0.762400 0.000000 + 21 C2 CQ 0 1 0 1 1 0.571600 0.000000 + 22 H2 H5 0 0 0 1 1 0.059800 0.000000 + 23 N3 NC 0 0 0 1 1 -0.741700 0.000000 + 24 C4 CB 0 0 0 1 1 0.380000 0.000000 + 25 C3* CT 0 0 0 1 1 0.071300 0.000000 + 26 H3* H1 0 0 0 1 1 0.098500 0.000000 + 27 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 282H2* HC 0 0 0 1 1 0.071800 0.000000 + 293H2* HC 0 0 0 1 1 0.071800 0.000000 + 30 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 31 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 21 23 + 23 24 + 6 25 + 25 26 + 25 27 + 27 28 + 27 29 + 25 30 + 30 31 + 9 27 + 15 24 + 11 24 diff --git a/src/data/amber_s/DC.frg b/src/data/amber_s/DC.frg new file mode 100644 index 0000000..751a320 --- /dev/null +++ b/src/data/amber_s/DC.frg @@ -0,0 +1,65 @@ +#D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group +$DC + 30 1 1 0 +D-CYTO + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 -0.011600 0.000000 + 12 H1* H2 0 0 0 1 1 0.196300 0.000000 + 13 N1 N* 0 1 0 1 1 -0.033900 0.000000 + 14 C6 CM 0 1 0 1 1 -0.018300 0.000000 + 15 H6 H4 0 0 0 1 1 0.229300 0.000000 + 16 C5 CM 0 1 0 1 1 -0.522200 0.000000 + 17 H5 HA 0 0 0 1 1 0.186300 0.000000 + 18 C4 CA 0 1 0 1 1 0.843900 0.000000 + 19 N4 N2 0 1 0 1 1 -0.977300 0.000000 + 202H4 H 0 0 0 1 1 0.431400 0.000000 + 213H4 H 0 0 0 1 1 0.431400 0.000000 + 22 N3 NC 0 0 0 1 1 -0.774800 0.000000 + 23 C2 C 0 1 0 1 1 0.795900 0.000000 + 24 O2 O 0 0 0 1 1 -0.654800 0.000000 + 25 C3* CT 0 0 0 1 1 0.071300 0.000000 + 26 H3* H1 0 0 0 1 1 0.098500 0.000000 + 27 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 282H2* HC 0 0 0 1 1 0.071800 0.000000 + 293H2* HC 0 0 0 1 1 0.071800 0.000000 + 30 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 8 25 + 25 26 + 25 27 + 27 28 + 27 29 + 25 30 + 11 27 + 13 23 diff --git a/src/data/amber_s/DC_3.frg b/src/data/amber_s/DC_3.frg new file mode 100644 index 0000000..cc98803 --- /dev/null +++ b/src/data/amber_s/DC_3.frg @@ -0,0 +1,67 @@ +#D-CYTOSINE - with 5' - phosphate group and 3' - OH group +$DC3 + 31 1 1 0 +D-CYTO + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 -0.011600 0.000000 + 12 H1* H2 0 0 0 1 1 0.196300 0.000000 + 13 N1 N* 0 1 0 1 1 -0.033900 0.000000 + 14 C6 CM 0 1 0 1 1 -0.018300 0.000000 + 15 H6 H4 0 0 0 1 1 0.229300 0.000000 + 16 C5 CM 0 1 0 1 1 -0.522200 0.000000 + 17 H5 HA 0 0 0 1 1 0.186300 0.000000 + 18 C4 CA 0 1 0 1 1 0.843900 0.000000 + 19 N4 N2 0 1 0 1 1 -0.977300 0.000000 + 202H4 H 0 0 0 1 1 0.431400 0.000000 + 213H4 H 0 0 0 1 1 0.431400 0.000000 + 22 N3 NC 0 0 0 1 1 -0.774800 0.000000 + 23 C2 C 0 1 0 1 1 0.795900 0.000000 + 24 O2 O 0 0 0 1 1 -0.654800 0.000000 + 25 C3* CT 0 0 0 1 1 0.071300 0.000000 + 26 H3* H1 0 0 0 1 1 0.098500 0.000000 + 27 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 282H2* HC 0 0 0 1 1 0.071800 0.000000 + 293H2* HC 0 0 0 1 1 0.071800 0.000000 + 30 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 31 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 8 25 + 25 26 + 25 27 + 27 28 + 27 29 + 25 30 + 30 31 + 11 27 + 13 23 diff --git a/src/data/amber_s/DC_5.frg b/src/data/amber_s/DC_5.frg new file mode 100644 index 0000000..fad2b2f --- /dev/null +++ b/src/data/amber_s/DC_5.frg @@ -0,0 +1,61 @@ +#D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group +$DC5 + 28 1 1 0 +D-CYTO + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 -0.011600 0.000000 + 10 H1* H2 0 0 0 1 1 0.196300 0.000000 + 11 N1 N* 0 1 0 1 1 -0.033900 0.000000 + 12 C6 CM 0 1 0 1 1 -0.018300 0.000000 + 13 H6 H4 0 0 0 1 1 0.229300 0.000000 + 14 C5 CM 0 1 0 1 1 -0.522200 0.000000 + 15 H5 HA 0 0 0 1 1 0.186300 0.000000 + 16 C4 CA 0 1 0 1 1 0.843900 0.000000 + 17 N4 N2 0 1 0 1 1 -0.977300 0.000000 + 182H4 H 0 0 0 1 1 0.431400 0.000000 + 193H4 H 0 0 0 1 1 0.431400 0.000000 + 20 N3 NC 0 0 0 1 1 -0.774800 0.000000 + 21 C2 C 0 1 0 1 1 0.795900 0.000000 + 22 O2 O 0 0 0 1 1 -0.654800 0.000000 + 23 C3* CT 0 0 0 1 1 0.071300 0.000000 + 24 H3* H1 0 0 0 1 1 0.098500 0.000000 + 25 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 262H2* HC 0 0 0 1 1 0.071800 0.000000 + 273H2* HC 0 0 0 1 1 0.071800 0.000000 + 28 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 6 23 + 23 24 + 23 25 + 25 26 + 25 27 + 23 28 + 9 25 + 11 21 diff --git a/src/data/amber_s/DC_M.frg b/src/data/amber_s/DC_M.frg new file mode 100644 index 0000000..777bf1a --- /dev/null +++ b/src/data/amber_s/DC_M.frg @@ -0,0 +1,63 @@ +#D-CYTOSINE - with 5' - OH group and 3' - OH group +$DCN + 29 1 1 0 +D-CYTO + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 -0.011600 0.000000 + 10 H1* H2 0 0 0 1 1 0.196300 0.000000 + 11 N1 N* 0 1 0 1 1 -0.033900 0.000000 + 12 C6 CM 0 1 0 1 1 -0.018300 0.000000 + 13 H6 H4 0 0 0 1 1 0.229300 0.000000 + 14 C5 CM 0 1 0 1 1 -0.522200 0.000000 + 15 H5 HA 0 0 0 1 1 0.186300 0.000000 + 16 C4 CA 0 1 0 1 1 0.843900 0.000000 + 17 N4 N2 0 1 0 1 1 -0.977300 0.000000 + 182H4 H 0 0 0 1 1 0.431400 0.000000 + 193H4 H 0 0 0 1 1 0.431400 0.000000 + 20 N3 NC 0 0 0 1 1 -0.774800 0.000000 + 21 C2 C 0 1 0 1 1 0.795900 0.000000 + 22 O2 O 0 0 0 1 1 -0.654800 0.000000 + 23 C3* CT 0 0 0 1 1 0.071300 0.000000 + 24 H3* H1 0 0 0 1 1 0.098500 0.000000 + 25 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 262H2* HC 0 0 0 1 1 0.071800 0.000000 + 273H2* HC 0 0 0 1 1 0.071800 0.000000 + 28 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 29 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 6 23 + 23 24 + 23 25 + 25 26 + 25 27 + 23 28 + 28 29 + 9 25 + 11 21 diff --git a/src/data/amber_s/DG.frg b/src/data/amber_s/DG.frg new file mode 100644 index 0000000..e888a87 --- /dev/null +++ b/src/data/amber_s/DG.frg @@ -0,0 +1,72 @@ +#D-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group +$DG + 33 1 1 0 +D-GUAN + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 0.035800 0.000000 + 12 H1* H2 0 0 0 1 1 0.174600 0.000000 + 13 N9 N* 0 1 0 1 1 0.057700 0.000000 + 14 C8 CK 0 1 0 1 1 0.073600 0.000000 + 15 H8 H5 0 0 0 1 1 0.199700 0.000000 + 16 N7 NB 0 0 0 1 1 -0.572500 0.000000 + 17 C5 CB 0 0 0 1 1 0.199100 0.000000 + 18 C6 C 0 1 0 1 1 0.491800 0.000000 + 19 O6 O 0 0 0 1 1 -0.569900 0.000000 + 20 N1 NA 0 1 0 1 1 -0.505300 0.000000 + 21 H1 H 0 0 0 1 1 0.352000 0.000000 + 22 C2 CA 0 1 0 1 1 0.743200 0.000000 + 23 N2 N2 0 1 0 1 1 -0.923000 0.000000 + 242H2 H 0 0 0 1 1 0.423500 0.000000 + 253H2 H 0 0 0 1 1 0.423500 0.000000 + 26 N3 NC 0 0 0 1 1 -0.663600 0.000000 + 27 C4 CB 0 0 0 1 1 0.181400 0.000000 + 28 C3* CT 0 0 0 1 1 0.071300 0.000000 + 29 H3* H1 0 0 0 1 1 0.098500 0.000000 + 30 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 312H2* HC 0 0 0 1 1 0.071800 0.000000 + 323H2* HC 0 0 0 1 1 0.071800 0.000000 + 33 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 18 20 + 20 21 + 20 22 + 22 23 + 23 24 + 23 25 + 22 26 + 26 27 + 8 28 + 28 29 + 28 30 + 30 31 + 30 32 + 28 33 + 11 30 + 17 27 + 13 27 diff --git a/src/data/amber_s/DG_3.frg b/src/data/amber_s/DG_3.frg new file mode 100644 index 0000000..a8ff289 --- /dev/null +++ b/src/data/amber_s/DG_3.frg @@ -0,0 +1,74 @@ +#D-GUANOSINE - with 5' - phosphate group and 3' - OH group +$DG3 + 34 1 1 0 +D-GUAN + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 0.035800 0.000000 + 12 H1* H2 0 0 0 1 1 0.174600 0.000000 + 13 N9 N* 0 1 0 1 1 0.057700 0.000000 + 14 C8 CK 0 1 0 1 1 0.073600 0.000000 + 15 H8 H5 0 0 0 1 1 0.199700 0.000000 + 16 N7 NB 0 0 0 1 1 -0.572500 0.000000 + 17 C5 CB 0 0 0 1 1 0.199100 0.000000 + 18 C6 C 0 1 0 1 1 0.491800 0.000000 + 19 O6 O 0 0 0 1 1 -0.569900 0.000000 + 20 N1 NA 0 1 0 1 1 -0.505300 0.000000 + 21 H1 H 0 0 0 1 1 0.352000 0.000000 + 22 C2 CA 0 1 0 1 1 0.743200 0.000000 + 23 N2 N2 0 1 0 1 1 -0.923000 0.000000 + 242H2 H 0 0 0 1 1 0.423500 0.000000 + 253H2 H 0 0 0 1 1 0.423500 0.000000 + 26 N3 NC 0 0 0 1 1 -0.663600 0.000000 + 27 C4 CB 0 0 0 1 1 0.181400 0.000000 + 28 C3* CT 0 0 0 1 1 0.071300 0.000000 + 29 H3* H1 0 0 0 1 1 0.098500 0.000000 + 30 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 312H2* HC 0 0 0 1 1 0.071800 0.000000 + 323H2* HC 0 0 0 1 1 0.071800 0.000000 + 33 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 34 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 18 20 + 20 21 + 20 22 + 22 23 + 23 24 + 23 25 + 22 26 + 26 27 + 8 28 + 28 29 + 28 30 + 30 31 + 30 32 + 28 33 + 33 34 + 11 30 + 17 27 + 13 27 diff --git a/src/data/amber_s/DG_5.frg b/src/data/amber_s/DG_5.frg new file mode 100644 index 0000000..0cb2880 --- /dev/null +++ b/src/data/amber_s/DG_5.frg @@ -0,0 +1,68 @@ +#D-GUANOSINE - with 5' - OH end group and 3' - O(minus) group +$DG5 + 31 1 1 0 +D-GUAN + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 0.035800 0.000000 + 10 H1* H2 0 0 0 1 1 0.174600 0.000000 + 11 N9 N* 0 1 0 1 1 0.057700 0.000000 + 12 C8 CK 0 1 0 1 1 0.073600 0.000000 + 13 H8 H5 0 0 0 1 1 0.199700 0.000000 + 14 N7 NB 0 0 0 1 1 -0.572500 0.000000 + 15 C5 CB 0 0 0 1 1 0.199100 0.000000 + 16 C6 C 0 1 0 1 1 0.491800 0.000000 + 17 O6 O 0 0 0 1 1 -0.569900 0.000000 + 18 N1 NA 0 1 0 1 1 -0.505300 0.000000 + 19 H1 H 0 0 0 1 1 0.352000 0.000000 + 20 C2 CA 0 1 0 1 1 0.743200 0.000000 + 21 N2 N2 0 1 0 1 1 -0.923000 0.000000 + 222H2 H 0 0 0 1 1 0.423500 0.000000 + 233H2 H 0 0 0 1 1 0.423500 0.000000 + 24 N3 NC 0 0 0 1 1 -0.663600 0.000000 + 25 C4 CB 0 0 0 1 1 0.181400 0.000000 + 26 C3* CT 0 0 0 1 1 0.071300 0.000000 + 27 H3* H1 0 0 0 1 1 0.098500 0.000000 + 28 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 292H2* HC 0 0 0 1 1 0.071800 0.000000 + 303H2* HC 0 0 0 1 1 0.071800 0.000000 + 31 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 21 22 + 21 23 + 20 24 + 24 25 + 6 26 + 26 27 + 26 28 + 28 29 + 28 30 + 26 31 + 9 28 + 15 25 + 11 25 diff --git a/src/data/amber_s/DG_M.frg b/src/data/amber_s/DG_M.frg new file mode 100644 index 0000000..8275c8e --- /dev/null +++ b/src/data/amber_s/DG_M.frg @@ -0,0 +1,70 @@ +#D-GUANOSINE - with 5' - OH group and 3' - OH group +$DGN + 32 1 1 0 +D-GUAN + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 0.035800 0.000000 + 10 H1* H2 0 0 0 1 1 0.174600 0.000000 + 11 N9 N* 0 1 0 1 1 0.057700 0.000000 + 12 C8 CK 0 1 0 1 1 0.073600 0.000000 + 13 H8 H5 0 0 0 1 1 0.199700 0.000000 + 14 N7 NB 0 0 0 1 1 -0.572500 0.000000 + 15 C5 CB 0 0 0 1 1 0.199100 0.000000 + 16 C6 C 0 1 0 1 1 0.491800 0.000000 + 17 O6 O 0 0 0 1 1 -0.569900 0.000000 + 18 N1 NA 0 1 0 1 1 -0.505300 0.000000 + 19 H1 H 0 0 0 1 1 0.352000 0.000000 + 20 C2 CA 0 1 0 1 1 0.743200 0.000000 + 21 N2 N2 0 1 0 1 1 -0.923000 0.000000 + 222H2 H 0 0 0 1 1 0.423500 0.000000 + 233H2 H 0 0 0 1 1 0.423500 0.000000 + 24 N3 NC 0 0 0 1 1 -0.663600 0.000000 + 25 C4 CB 0 0 0 1 1 0.181400 0.000000 + 26 C3* CT 0 0 0 1 1 0.071300 0.000000 + 27 H3* H1 0 0 0 1 1 0.098500 0.000000 + 28 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 292H2* HC 0 0 0 1 1 0.071800 0.000000 + 303H2* HC 0 0 0 1 1 0.071800 0.000000 + 31 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 32 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 21 22 + 21 23 + 20 24 + 24 25 + 6 26 + 26 27 + 26 28 + 28 29 + 28 30 + 26 31 + 31 32 + 9 28 + 15 25 + 11 25 diff --git a/src/data/amber_s/DT.frg b/src/data/amber_s/DT.frg new file mode 100644 index 0000000..7b0b3bd --- /dev/null +++ b/src/data/amber_s/DT.frg @@ -0,0 +1,69 @@ +#D-THYMINE - with 5' - phosphate group and 3' - O(minus) group +$DT + 32 1 1 0 +D-THYM + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 0.068000 0.000000 + 12 H1* H2 0 0 0 1 1 0.180400 0.000000 + 13 N1 N* 0 1 0 1 1 -0.023900 0.000000 + 14 C6 CM 0 1 0 1 1 -0.220900 0.000000 + 15 H6 H4 0 0 0 1 1 0.260700 0.000000 + 16 C5 CM 0 1 0 1 1 0.002500 0.000000 + 17 C5M CT 0 0 0 1 1 -0.226900 0.000000 + 182H5M HC 0 0 0 1 1 0.077000 0.000000 + 193H5M HC 0 0 0 1 1 0.077000 0.000000 + 204H5M HC 0 0 0 1 1 0.077000 0.000000 + 21 C4 C 0 1 0 1 1 0.519400 0.000000 + 22 O4 O 0 0 0 1 1 -0.556300 0.000000 + 23 N3 NA 0 1 0 1 1 -0.434000 0.000000 + 24 H3 H 0 0 0 1 1 0.342000 0.000000 + 25 C2 C 0 1 0 1 1 0.567700 0.000000 + 26 O2 O 0 0 0 1 1 -0.588100 0.000000 + 27 C3* CT 0 0 0 1 1 0.071300 0.000000 + 28 H3* H1 0 0 0 1 1 0.098500 0.000000 + 29 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 302H2* HC 0 0 0 1 1 0.071800 0.000000 + 313H2* HC 0 0 0 1 1 0.071800 0.000000 + 32 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 17 19 + 17 20 + 16 21 + 21 22 + 21 23 + 23 24 + 23 25 + 25 26 + 8 27 + 27 28 + 27 29 + 29 30 + 29 31 + 27 32 + 11 29 + 13 25 diff --git a/src/data/amber_s/DT_3.frg b/src/data/amber_s/DT_3.frg new file mode 100644 index 0000000..4b8c855 --- /dev/null +++ b/src/data/amber_s/DT_3.frg @@ -0,0 +1,71 @@ +#D-THYMINE - with 5' - phosphate group and 3' - OH group +$DT3 + 33 1 1 0 +D-THYM + 1 P P 3 0 0 1 1 1.165900 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776100 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776100 0.000000 + 4 O5* OS 0 0 0 1 1 -0.495400 0.000000 + 5 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 62H5* H1 0 0 0 1 1 0.075400 0.000000 + 73H5* H1 0 0 0 1 1 0.075400 0.000000 + 8 C4* CT 0 0 0 1 1 0.162900 0.000000 + 9 H4* H1 0 0 0 1 1 0.117600 0.000000 + 10 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 11 C1* CT 0 0 0 1 1 0.068000 0.000000 + 12 H1* H2 0 0 0 1 1 0.180400 0.000000 + 13 N1 N* 0 1 0 1 1 -0.023900 0.000000 + 14 C6 CM 0 1 0 1 1 -0.220900 0.000000 + 15 H6 H4 0 0 0 1 1 0.260700 0.000000 + 16 C5 CM 0 1 0 1 1 0.002500 0.000000 + 17 C5M CT 0 0 0 1 1 -0.226900 0.000000 + 182H5M HC 0 0 0 1 1 0.077000 0.000000 + 193H5M HC 0 0 0 1 1 0.077000 0.000000 + 204H5M HC 0 0 0 1 1 0.077000 0.000000 + 21 C4 C 0 1 0 1 1 0.519400 0.000000 + 22 O4 O 0 0 0 1 1 -0.556300 0.000000 + 23 N3 NA 0 1 0 1 1 -0.434000 0.000000 + 24 H3 H 0 0 0 1 1 0.342000 0.000000 + 25 C2 C 0 1 0 1 1 0.567700 0.000000 + 26 O2 O 0 0 0 1 1 -0.588100 0.000000 + 27 C3* CT 0 0 0 1 1 0.071300 0.000000 + 28 H3* H1 0 0 0 1 1 0.098500 0.000000 + 29 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 302H2* HC 0 0 0 1 1 0.071800 0.000000 + 313H2* HC 0 0 0 1 1 0.071800 0.000000 + 32 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 33 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 17 19 + 17 20 + 16 21 + 21 22 + 21 23 + 23 24 + 23 25 + 25 26 + 8 27 + 27 28 + 27 29 + 29 30 + 29 31 + 27 32 + 32 33 + 11 29 + 13 25 diff --git a/src/data/amber_s/DT_5.frg b/src/data/amber_s/DT_5.frg new file mode 100644 index 0000000..cbb0a59 --- /dev/null +++ b/src/data/amber_s/DT_5.frg @@ -0,0 +1,65 @@ +#D-THYMINE - with 5' - OH end group and 3' - O(minus) +$DT5 + 30 1 1 0 +D-THYM + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 0.068000 0.000000 + 10 H1* H2 0 0 0 1 1 0.180400 0.000000 + 11 N1 N* 0 1 0 1 1 -0.023900 0.000000 + 12 C6 CM 0 1 0 1 1 -0.220900 0.000000 + 13 H6 H4 0 0 0 1 1 0.260700 0.000000 + 14 C5 CM 0 1 0 1 1 0.002500 0.000000 + 15 C5M CT 0 0 0 1 1 -0.226900 0.000000 + 162H5M HC 0 0 0 1 1 0.077000 0.000000 + 173H5M HC 0 0 0 1 1 0.077000 0.000000 + 184H5M HC 0 0 0 1 1 0.077000 0.000000 + 19 C4 C 0 1 0 1 1 0.519400 0.000000 + 20 O4 O 0 0 0 1 1 -0.556300 0.000000 + 21 N3 NA 0 1 0 1 1 -0.434000 0.000000 + 22 H3 H 0 0 0 1 1 0.342000 0.000000 + 23 C2 C 0 1 0 1 1 0.567700 0.000000 + 24 O2 O 0 0 0 1 1 -0.588100 0.000000 + 25 C3* CT 0 0 0 1 1 0.071300 0.000000 + 26 H3* H1 0 0 0 1 1 0.098500 0.000000 + 27 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 282H2* HC 0 0 0 1 1 0.071800 0.000000 + 293H2* HC 0 0 0 1 1 0.071800 0.000000 + 30 O3* OS 3 0 0 1 1 -0.523200 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 15 17 + 15 18 + 14 19 + 19 20 + 19 21 + 21 22 + 21 23 + 23 24 + 6 25 + 25 26 + 25 27 + 27 28 + 27 29 + 25 30 + 9 27 + 11 23 diff --git a/src/data/amber_s/DT_M.frg b/src/data/amber_s/DT_M.frg new file mode 100644 index 0000000..eb5abc7 --- /dev/null +++ b/src/data/amber_s/DT_M.frg @@ -0,0 +1,67 @@ +#D-THYMINE - with 5' - OH group and 3' - OH group +$DTN + 31 1 1 0 +D-THYM + 1 H5T HO 0 0 0 1 1 0.442200 0.000000 + 2 O5* OH 0 0 0 1 1 -0.631800 0.000000 + 3 C5* CT 0 0 0 1 1 -0.006900 0.000000 + 42H5* H1 0 0 0 1 1 0.075400 0.000000 + 53H5* H1 0 0 0 1 1 0.075400 0.000000 + 6 C4* CT 0 0 0 1 1 0.162900 0.000000 + 7 H4* H1 0 0 0 1 1 0.117600 0.000000 + 8 O4* OS 0 0 0 1 1 -0.369100 0.000000 + 9 C1* CT 0 0 0 1 1 0.068000 0.000000 + 10 H1* H2 0 0 0 1 1 0.180400 0.000000 + 11 N1 N* 0 1 0 1 1 -0.023900 0.000000 + 12 C6 CM 0 1 0 1 1 -0.220900 0.000000 + 13 H6 H4 0 0 0 1 1 0.260700 0.000000 + 14 C5 CM 0 1 0 1 1 0.002500 0.000000 + 15 C5M CT 0 0 0 1 1 -0.226900 0.000000 + 162H5M HC 0 0 0 1 1 0.077000 0.000000 + 173H5M HC 0 0 0 1 1 0.077000 0.000000 + 184H5M HC 0 0 0 1 1 0.077000 0.000000 + 19 C4 C 0 1 0 1 1 0.519400 0.000000 + 20 O4 O 0 0 0 1 1 -0.556300 0.000000 + 21 N3 NA 0 1 0 1 1 -0.434000 0.000000 + 22 H3 H 0 0 0 1 1 0.342000 0.000000 + 23 C2 C 0 1 0 1 1 0.567700 0.000000 + 24 O2 O 0 0 0 1 1 -0.588100 0.000000 + 25 C3* CT 0 0 0 1 1 0.071300 0.000000 + 26 H3* H1 0 0 0 1 1 0.098500 0.000000 + 27 C2* CT 0 0 0 1 1 -0.085400 0.000000 + 282H2* HC 0 0 0 1 1 0.071800 0.000000 + 293H2* HC 0 0 0 1 1 0.071800 0.000000 + 30 O3* OH 0 0 0 1 1 -0.654900 0.000000 + 31 H3T HO 0 0 0 1 1 0.439600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 15 17 + 15 18 + 14 19 + 19 20 + 19 21 + 21 22 + 21 23 + 23 24 + 6 25 + 25 26 + 25 27 + 27 28 + 27 29 + 25 30 + 30 31 + 9 27 + 11 23 diff --git a/src/data/amber_s/FE.frg b/src/data/amber_s/FE.frg new file mode 100644 index 0000000..51599ea --- /dev/null +++ b/src/data/amber_s/FE.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$FE + 1 1 1 0 +FE + 1FE FE 3 0 0 1 1 0.000000 0.000000 diff --git a/src/data/amber_s/GLH.frg b/src/data/amber_s/GLH.frg new file mode 100644 index 0000000..2bbebcf --- /dev/null +++ b/src/data/amber_s/GLH.frg @@ -0,0 +1,34 @@ +$GLH + 16 1 1 0 +GLH + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 0.014500 0.000000 + 4 HA H1 0 0 0 1 1 0.077900 0.000000 + 5 CB CT 0 0 0 1 1 -0.007100 0.000000 + 62HB HC 0 0 0 1 1 0.025600 0.000000 + 73HB HC 0 0 0 1 1 0.025600 0.000000 + 8 CG CT 0 0 0 1 1 -0.017400 0.000000 + 92HG HC 0 0 0 1 1 0.043000 0.000000 + 103HG HC 0 0 0 1 1 0.043000 0.000000 + 11 CD C 0 1 0 1 1 0.680100 0.000000 + 12 OE1 O 0 0 0 1 1 -0.583800 0.000000 + 13 OE2 OH 0 0 0 1 1 -0.651100 0.000000 + 14 HE2 HO 0 0 0 1 1 0.464100 0.000000 + 15 C C 2 1 0 1 1 0.597300 0.000000 + 16 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 5 + 7 5 + 8 5 + 9 8 + 10 8 + 11 8 + 12 11 + 13 11 + 14 13 + 15 3 + 16 15 diff --git a/src/data/amber_s/GLH.sgm b/src/data/amber_s/GLH.sgm new file mode 100644 index 0000000..d9f74ca --- /dev/null +++ b/src/data/amber_s/GLH.sgm @@ -0,0 +1,181 @@ +# +$GLH + 4.600000 + 16 15 24 32 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT 0.014500 0.000000 + 4 HA 0 0 0 1 1 + H1 0.077900 0.000000 + 5 CB 0 0 0 1 1 + CT -0.007100 0.000000 + 62HB 0 0 0 1 1 + HC 0.025600 0.000000 + 73HB 0 0 0 1 1 + HC 0.025600 0.000000 + 8 CG 0 0 0 1 1 + CT -0.017400 0.000000 + 92HG 0 0 0 1 1 + HC 0.043000 0.000000 + 103HG 0 0 0 1 1 + HC 0.043000 0.000000 + 11 CD 0 1 0 1 1 + C 0.680100 0.000000 + 12 OE1 0 0 0 1 1 + O -0.583800 0.000000 + 13 OE2 0 0 0 1 1 + OH -0.651100 0.000000 + 14 HE2 0 0 0 1 1 + HO 0.464100 0.000000 + 15 C 2 1 0 1 1 + C 0.597300 0.000000 + 16 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 15 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 8 10 0 0 + 0.000000 0.00000E+00 + 11 8 11 0 0 + 0.000000 0.00000E+00 + 12 11 12 0 0 + 0.000000 0.00000E+00 + 13 11 13 0 0 + 0.000000 0.00000E+00 + 14 13 14 0 0 + 0.000000 0.00000E+00 + 15 15 16 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 15 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 15 0 0 + 0.000000 0.00000E+00 + 7 5 3 15 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 5 8 9 0 0 + 0.000000 0.00000E+00 + 15 5 8 10 0 0 + 0.000000 0.00000E+00 + 16 5 8 11 0 0 + 0.000000 0.00000E+00 + 17 9 8 10 0 0 + 0.000000 0.00000E+00 + 18 9 8 11 0 0 + 0.000000 0.00000E+00 + 19 10 8 11 0 0 + 0.000000 0.00000E+00 + 20 8 11 12 0 0 + 0.000000 0.00000E+00 + 21 8 11 13 0 0 + 0.000000 0.00000E+00 + 22 12 11 13 0 0 + 0.000000 0.00000E+00 + 23 11 13 14 0 0 + 0.000000 0.00000E+00 + 24 3 15 16 0 0 + 0.000000 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0 + 0 0.000000 0.00000E+00 + 25 5 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 26 5 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 27 9 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 28 9 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 29 10 8 11 12 0 0 + 0 0.000000 0.00000E+00 + 30 10 8 11 13 0 0 + 0 0.000000 0.00000E+00 + 31 8 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 32 12 11 13 14 0 0 + 0 0.000000 0.00000E+00 + 1 8 13 11 12 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/GLN.frg b/src/data/amber_s/GLN.frg new file mode 100644 index 0000000..b210913 --- /dev/null +++ b/src/data/amber_s/GLN.frg @@ -0,0 +1,36 @@ +$GLN + 17 1 1 0 +GLN + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.003100 0.000000 + 4 HA H1 0 0 0 1 1 0.085000 0.000000 + 5 CB CT 0 0 0 1 1 -0.003600 0.000000 + 62HB HC 0 0 0 1 1 0.017100 0.000000 + 73HB HC 0 0 0 1 1 0.017100 0.000000 + 8 CG CT 0 0 0 1 1 -0.064500 0.000000 + 92HG HC 0 0 0 1 1 0.035200 0.000000 + 103HG HC 0 0 0 1 1 0.035200 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-0.069900 0.000000 + 152HD HC 0 0 0 1 1 0.019600 0.000000 + 163HD HC 0 0 0 1 1 0.019600 0.000000 + 174HD HC 0 0 0 1 1 0.019600 0.000000 + 18 C C 0 1 0 1 1 0.834300 0.000000 + 19 O O2 0 0 0 1 1 -0.819000 0.000000 + 20 OXT O2 0 0 0 1 1 -0.819000 0.000000 + 2 1 3 18 19 + 18 20 + 4 3 5 7 8 + 5 6 + 9 7 10 + 5 11 14 15 + 12 11 13 + 16 14 17 diff --git a/src/data/amber_s/ILE_C.sgm b/src/data/amber_s/ILE_C.sgm new file mode 100644 index 0000000..9e1ce95 --- /dev/null +++ b/src/data/amber_s/ILE_C.sgm @@ -0,0 +1,243 @@ +# +$ILE_C + 4.600000 + 20 19 34 45 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.382100 0.000000 + 2 H 0 0 0 1 1 + H 0.268100 0.000000 + 3 CA 0 0 0 1 1 + CT -0.310000 0.000000 + 4 HA 0 0 0 1 1 + H1 0.137500 0.000000 + 5 CB 0 0 0 1 1 + CT 0.036300 0.000000 + 6 HB 0 0 0 1 1 + HC 0.076600 0.000000 + 7 CG2 0 0 0 1 1 + CT -0.349800 0.000000 + 82HG2 0 0 0 1 1 + HC 0.102100 0.000000 + 93HG2 0 0 0 1 1 + HC 0.102100 0.000000 + 104HG2 0 0 0 1 1 + HC 0.102100 0.000000 + 11 CG1 0 0 0 1 1 + CT 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0.000000 + 113HG2 HC 0 0 0 1 1 0.094700 0.000000 + 124HG2 HC 0 0 0 1 1 0.094700 0.000000 + 13 CG1 CT 0 0 0 1 1 -0.038700 0.000000 + 142HG1 HC 0 0 0 1 1 0.020100 0.000000 + 153HG1 HC 0 0 0 1 1 0.020100 0.000000 + 16 CD CT 0 0 0 1 1 -0.090800 0.000000 + 172HD HC 0 0 0 1 1 0.022600 0.000000 + 183HD HC 0 0 0 1 1 0.022600 0.000000 + 194HD HC 0 0 0 1 1 0.022600 0.000000 + 20 C C 2 1 0 1 1 0.612300 0.000000 + 21 O O 0 0 0 1 1 -0.571300 0.000000 + 2 1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 9 + 11 9 + 12 9 + 13 7 + 14 13 + 15 13 + 16 13 + 17 16 + 18 16 + 19 16 + 20 5 + 21 20 diff --git a/src/data/amber_s/ILE_N.sgm b/src/data/amber_s/ILE_N.sgm new file mode 100644 index 0000000..6fa7217 --- /dev/null +++ b/src/data/amber_s/ILE_N.sgm @@ -0,0 +1,257 @@ +# +$ILE_N + 4.600000 + 21 20 37 48 0 0 1 1 + 0.000000 + 1 N 0 0 0 1 1 + N3 0.031100 0.000000 + 22H 0 0 0 1 1 + H 0.232900 0.000000 + 33H 0 0 0 1 1 + H 0.232900 0.000000 + 44H 0 0 0 1 1 + H 0.232900 0.000000 + 5 CA 0 0 0 1 1 + CT 0.025700 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file mode 100644 index 0000000..b82c820 --- /dev/null +++ b/src/data/amber_s/IM.frg @@ -0,0 +1,4 @@ +$IM + 1 1 1 0 +IM + 1CL- IM 0 0 0 1 1 -1.000000 0.000000 diff --git a/src/data/amber_s/IM.sgm b/src/data/amber_s/IM.sgm new file mode 100644 index 0000000..0a5ff2f --- /dev/null +++ b/src/data/amber_s/IM.sgm @@ -0,0 +1,7 @@ +# This is an automatically generated segment file +# + 4.600000 + 1 0 0 0 0 0 1 1 + 0.000000 + 1IM 0 0 0 1 1 + IM -1.000000 0.000000 diff --git a/src/data/amber_s/IP.frg b/src/data/amber_s/IP.frg new file mode 100644 index 0000000..c9aa98e --- /dev/null +++ b/src/data/amber_s/IP.frg @@ -0,0 +1,4 @@ +$IP + 1 1 1 0 +IP + 1NA+ IP 0 0 0 1 1 1.000000 0.000000 diff --git a/src/data/amber_s/K.frg b/src/data/amber_s/K.frg new file mode 100644 index 0000000..ee76e14 --- /dev/null +++ b/src/data/amber_s/K.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$K + 1 1 1 0 +K + 1 K K 0 0 0 1 1 1.000000 0.000000 diff --git a/src/data/amber_s/K.sgm b/src/data/amber_s/K.sgm new file mode 100644 index 0000000..2b25bfd --- /dev/null +++ b/src/data/amber_s/K.sgm @@ -0,0 +1,7 @@ +# This is an automatically generated segment file +# + 4.600000 + 1 0 0 0 0 0 1 1 + 0.000000 + 1 K 0 0 0 1 1 + K 1.000000 0.000000 diff --git a/src/data/amber_s/LEU.frg b/src/data/amber_s/LEU.frg new file mode 100644 index 0000000..047bff5 --- /dev/null +++ b/src/data/amber_s/LEU.frg @@ -0,0 +1,40 @@ +$LEU + 19 1 1 0 +LEU + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.051800 0.000000 + 4 HA H1 0 0 0 1 1 0.092200 0.000000 + 5 CB CT 0 0 0 1 1 -0.110200 0.000000 + 62HB HC 0 0 0 1 1 0.045700 0.000000 + 73HB HC 0 0 0 1 1 0.045700 0.000000 + 8 CG CT 0 0 0 1 1 0.353100 0.000000 + 9 HG HC 0 0 0 1 1 -0.036100 0.000000 + 10 CD1 CT 0 0 0 1 1 -0.412100 0.000000 + 112HD1 HC 0 0 0 1 1 0.100000 0.000000 + 123HD1 HC 0 0 0 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a/src/data/amber_s/LYN.frg b/src/data/amber_s/LYN.frg new file mode 100644 index 0000000..881f551 --- /dev/null +++ b/src/data/amber_s/LYN.frg @@ -0,0 +1,44 @@ +$LYN + 21 1 1 0 +LYN + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.072000 0.000000 + 4 HA H1 0 0 0 1 1 0.099400 0.000000 + 5 CB CT 0 0 0 1 1 -0.048400 0.000000 + 62HB HC 0 0 0 1 1 0.034000 0.000000 + 73HB HC 0 0 0 1 1 0.034000 0.000000 + 8 CG CT 0 0 0 1 1 0.066100 0.000000 + 92HG HC 0 0 0 1 1 0.010400 0.000000 + 103HG HC 0 0 0 1 1 0.010400 0.000000 + 11 CD CT 0 0 0 1 1 -0.037600 0.000000 + 122HD HC 0 0 0 1 1 0.011500 0.000000 + 133HD HC 0 0 0 1 1 0.011500 0.000000 + 14 CE CT 0 0 0 1 1 0.326000 0.000000 + 152HE HP 0 0 0 1 1 -0.033500 0.000000 + 163HE HP 0 0 0 1 1 -0.033500 0.000000 + 17 NZ N3 0 0 0 1 1 -1.035800 0.000000 + 182HZ H 0 0 0 1 1 0.386000 0.000000 + 193HZ H 0 0 0 1 1 0.386000 0.000000 + 20 C C 2 1 0 1 1 0.597300 0.000000 + 21 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 + 3 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b/src/data/amber_s/LYS_C.frg new file mode 100644 index 0000000..98ee2b7 --- /dev/null +++ b/src/data/amber_s/LYS_C.frg @@ -0,0 +1,34 @@ +$LYS_C + 23 1 1 0 +LYS_C + 1 N N 1 1 0 1 1 -0.348100 0.000000 + 2 H H 0 0 0 1 1 0.276400 0.000000 + 3 CA CT 0 0 0 1 1 -0.290300 0.000000 + 4 HA H1 0 0 0 1 1 0.143800 0.000000 + 5 CB CT 0 0 0 1 1 -0.053800 0.000000 + 62HB HC 0 0 0 1 1 0.048200 0.000000 + 73HB HC 0 0 0 1 1 0.048200 0.000000 + 8 CG CT 0 0 0 1 1 0.022700 0.000000 + 92HG HC 0 0 0 1 1 0.013400 0.000000 + 103HG HC 0 0 0 1 1 0.013400 0.000000 + 11 CD CT 0 0 0 1 1 -0.039200 0.000000 + 122HD HC 0 0 0 1 1 0.061100 0.000000 + 133HD HC 0 0 0 1 1 0.061100 0.000000 + 14 CE CT 0 0 0 1 1 -0.017600 0.000000 + 152HE HP 0 0 0 1 1 0.112100 0.000000 + 163HE HP 0 0 0 1 1 0.112100 0.000000 + 17 NZ N3 0 0 0 1 1 -0.374100 0.000000 + 182HZ H 0 0 0 1 1 0.337400 0.000000 + 193HZ H 0 0 0 1 1 0.337400 0.000000 + 204HZ H 0 0 0 1 1 0.337400 0.000000 + 21 C C 0 1 0 1 1 0.848800 0.000000 + 22 O O2 0 0 0 1 1 -0.825200 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19 0 0 + 0 0.000000 0.00000E+00 + 54 16 14 17 20 0 0 + 0 0.000000 0.00000E+00 + 1 3 22 21 23 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/LYS_N.frg b/src/data/amber_s/LYS_N.frg new file mode 100644 index 0000000..62d4590 --- /dev/null +++ b/src/data/amber_s/LYS_N.frg @@ -0,0 +1,50 @@ +$LYS_N + 24 1 1 0 +LYS_N + 1 N N3 0 0 0 1 1 0.096600 0.000000 + 22H H 0 0 0 1 1 0.216500 0.000000 + 33H H 0 0 0 1 1 0.216500 0.000000 + 44H H 0 0 0 1 1 0.216500 0.000000 + 5 CA CT 0 0 0 1 1 -0.001500 0.000000 + 6 HA HP 0 0 0 1 1 0.118000 0.000000 + 7 CB CT 0 0 0 1 1 0.021200 0.000000 + 82HB HC 0 0 0 1 1 0.028300 0.000000 + 93HB HC 0 0 0 1 1 0.028300 0.000000 + 10 CG CT 0 0 0 1 1 -0.004800 0.000000 + 112HG HC 0 0 0 1 1 0.012100 0.000000 + 123HG HC 0 0 0 1 1 0.012100 0.000000 + 13 CD CT 0 0 0 1 1 -0.060800 0.000000 + 142HD HC 0 0 0 1 1 0.063300 0.000000 + 153HD HC 0 0 0 1 1 0.063300 0.000000 + 16 CE CT 0 0 0 1 1 -0.018100 0.000000 + 172HE HP 0 0 0 1 1 0.117100 0.000000 + 183HE HP 0 0 0 1 1 0.117100 0.000000 + 19 NZ N3 0 0 0 1 1 -0.376400 0.000000 + 202HZ H 0 0 0 1 1 0.338200 0.000000 + 213HZ H 0 0 0 1 1 0.338200 0.000000 + 224HZ H 0 0 0 1 1 0.338200 0.000000 + 23 C C 2 1 0 1 1 0.721400 0.000000 + 24 O O 0 0 0 1 1 -0.601300 0.000000 + 2 1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 7 + 11 10 + 12 10 + 13 10 + 14 13 + 15 13 + 16 13 + 17 16 + 18 16 + 19 16 + 20 19 + 21 19 + 22 19 + 23 5 + 24 23 diff --git a/src/data/amber_s/LYS_N.sgm b/src/data/amber_s/LYS_N.sgm new file mode 100644 index 0000000..c7da530 --- /dev/null +++ b/src/data/amber_s/LYS_N.sgm @@ -0,0 +1,299 @@ +# +$LYS_N + 4.600000 + 24 23 43 57 0 0 1 1 + 0.000000 + 1 N 0 0 0 1 1 + N3 0.096600 0.000000 + 22H 0 0 0 1 1 + H 0.216500 0.000000 + 33H 0 0 0 1 1 + H 0.216500 0.000000 + 44H 0 0 0 1 1 + H 0.216500 0.000000 + 5 CA 0 0 0 1 1 + CT -0.001500 0.000000 + 6 HA 0 0 0 1 1 + HP 0.118000 0.000000 + 7 CB 0 0 0 1 1 + CT 0.021200 0.000000 + 82HB 0 0 0 1 1 + HC 0.028300 0.000000 + 93HB 0 0 0 1 1 + HC 0.028300 0.000000 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charges are crude guestimations +# +$Li + 1 1 1 0 +Li + 1Li Li 0 0 0 1 1 1.000000 0.000000 diff --git a/src/data/amber_s/MET.frg b/src/data/amber_s/MET.frg new file mode 100644 index 0000000..d278212 --- /dev/null +++ b/src/data/amber_s/MET.frg @@ -0,0 +1,36 @@ +$MET + 17 1 1 0 +MET + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.023700 0.000000 + 4 HA H1 0 0 0 1 1 0.088000 0.000000 + 5 CB CT 0 0 0 1 1 0.034200 0.000000 + 62HB HC 0 0 0 1 1 0.024100 0.000000 + 73HB HC 0 0 0 1 1 0.024100 0.000000 + 8 CG CT 0 0 0 1 1 0.001800 0.000000 + 92HG H1 0 0 0 1 1 0.044000 0.000000 + 103HG H1 0 0 0 1 1 0.044000 0.000000 + 11 SD S 0 0 0 1 1 -0.273700 0.000000 + 12 CE CT 0 0 0 1 1 -0.053600 0.000000 + 132HE H1 0 0 0 1 1 0.068400 0.000000 + 143HE H1 0 0 0 1 1 0.068400 0.000000 + 154HE H1 0 0 0 1 1 0.068400 0.000000 + 16 C C 2 1 0 1 1 0.597300 0.000000 + 17 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 5 + 7 5 + 8 5 + 9 8 + 10 8 + 11 8 + 12 11 + 13 12 + 14 12 + 15 12 + 16 3 + 17 16 diff --git a/src/data/amber_s/MET.sgm b/src/data/amber_s/MET.sgm new file mode 100644 index 0000000..fea25c0 --- /dev/null +++ b/src/data/amber_s/MET.sgm @@ -0,0 +1,189 @@ +# +$MET + 4.600000 + 17 16 27 30 0 4 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT -0.023700 0.000000 + 4 HA 0 0 0 1 1 + H1 0.088000 0.000000 + 5 CB 0 0 0 1 1 + CT 0.034200 0.000000 + 62HB 0 0 0 1 1 + HC 0.024100 0.000000 + 73HB 0 0 0 1 1 + HC 0.024100 0.000000 + 8 CG 0 0 0 1 1 + CT 0.001800 0.000000 + 92HG 0 0 0 1 1 + H1 0.044000 0.000000 + 103HG 0 0 0 1 1 + H1 0.044000 0.000000 + 11 SD 0 0 0 1 1 + S -0.273700 0.000000 + 12 CE 0 0 0 1 1 + CT -0.053600 0.000000 + 132HE 0 0 0 1 1 + H1 0.068400 0.000000 + 143HE 0 0 0 1 1 + H1 0.068400 0.000000 + 154HE 0 0 0 1 1 + H1 0.068400 0.000000 + 16 C 2 1 0 1 1 + C 0.597300 0.000000 + 17 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 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b/src/data/amber_s/MET_C.frg new file mode 100644 index 0000000..ea5407c --- /dev/null +++ b/src/data/amber_s/MET_C.frg @@ -0,0 +1,38 @@ +$MET_C + 18 1 1 0 +MET_C + 1 N N 1 1 0 1 1 -0.382100 0.000000 + 2 H H 0 0 0 1 1 0.268100 0.000000 + 3 CA CT 0 0 0 1 1 -0.259700 0.000000 + 4 HA H1 0 0 0 1 1 0.127700 0.000000 + 5 CB CT 0 0 0 1 1 -0.023600 0.000000 + 62HB HC 0 0 0 1 1 0.048000 0.000000 + 73HB HC 0 0 0 1 1 0.048000 0.000000 + 8 CG CT 0 0 0 1 1 0.049200 0.000000 + 92HG H1 0 0 0 1 1 0.031700 0.000000 + 103HG H1 0 0 0 1 1 0.031700 0.000000 + 11 SD S 0 0 0 1 1 -0.269200 0.000000 + 12 CE CT 0 0 0 1 1 -0.037600 0.000000 + 132HE H1 0 0 0 1 1 0.062500 0.000000 + 143HE H1 0 0 0 1 1 0.062500 0.000000 + 154HE H1 0 0 0 1 1 0.062500 0.000000 + 16 C C 0 1 0 1 1 0.801300 0.000000 + 17 O O2 0 0 0 1 1 -0.810500 0.000000 + 18 OXT O2 0 0 0 1 1 -0.810500 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 5 + 7 5 + 8 5 + 9 8 + 10 8 + 11 8 + 12 11 + 13 12 + 14 12 + 15 12 + 16 3 + 17 16 + 18 16 diff --git a/src/data/amber_s/MET_C.sgm b/src/data/amber_s/MET_C.sgm new file mode 100644 index 0000000..e57409a --- /dev/null +++ b/src/data/amber_s/MET_C.sgm @@ -0,0 +1,201 @@ +# +$MET_C + 4.600000 + 18 17 29 33 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.382100 0.000000 + 2 H 0 0 0 1 1 + H 0.268100 0.000000 + 3 CA 0 0 0 1 1 + CT -0.259700 0.000000 + 4 HA 0 0 0 1 1 + H1 0.127700 0.000000 + 5 CB 0 0 0 1 1 + CT -0.023600 0.000000 + 62HB 0 0 0 1 1 + HC 0.048000 0.000000 + 73HB 0 0 0 1 1 + HC 0.048000 0.000000 + 8 CG 0 0 0 1 1 + CT 0.049200 0.000000 + 92HG 0 0 0 1 1 + H1 0.031700 0.000000 + 103HG 0 0 0 1 1 + H1 0.031700 0.000000 + 11 SD 0 0 0 1 1 + S -0.269200 0.000000 + 12 CE 0 0 0 1 1 + CT -0.037600 0.000000 + 132HE 0 0 0 1 1 + H1 0.062500 0.000000 + 143HE 0 0 0 1 1 + H1 0.062500 0.000000 + 154HE 0 0 0 1 1 + H1 0.062500 0.000000 + 16 C 0 1 0 1 1 + C 0.801300 0.000000 + 17 O 0 0 0 1 1 + O2 -0.810500 0.000000 + 18 OXT 0 0 0 1 1 + O2 -0.810500 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 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+ 0 0.000000 0.00000E+00 + 32 8 11 12 14 0 0 + 0 0.000000 0.00000E+00 + 33 8 11 12 15 0 0 + 0 0.000000 0.00000E+00 + 1 3 17 16 18 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/MET_N.frg b/src/data/amber_s/MET_N.frg new file mode 100644 index 0000000..126daff --- /dev/null +++ b/src/data/amber_s/MET_N.frg @@ -0,0 +1,40 @@ +$MET_N + 19 1 1 0 +MET_N + 1 N N3 0 0 0 1 1 0.159200 0.000000 + 22H H 0 0 0 1 1 0.198400 0.000000 + 33H H 0 0 0 1 1 0.198400 0.000000 + 44H H 0 0 0 1 1 0.198400 0.000000 + 5 CA CT 0 0 0 1 1 0.022100 0.000000 + 6 HA HP 0 0 0 1 1 0.111600 0.000000 + 7 CB CT 0 0 0 1 1 0.086500 0.000000 + 82HB HC 0 0 0 1 1 0.012500 0.000000 + 93HB HC 0 0 0 1 1 0.012500 0.000000 + 10 CG CT 0 0 0 1 1 0.033400 0.000000 + 112HG H1 0 0 0 1 1 0.029200 0.000000 + 123HG H1 0 0 0 1 1 0.029200 0.000000 + 13 SD S 0 0 0 1 1 -0.277400 0.000000 + 14 CE CT 0 0 0 1 1 -0.034100 0.000000 + 152HE H1 0 0 0 1 1 0.059700 0.000000 + 163HE H1 0 0 0 1 1 0.059700 0.000000 + 174HE H1 0 0 0 1 1 0.059700 0.000000 + 18 C C 2 1 0 1 1 0.612300 0.000000 + 19 O O 0 0 0 1 1 -0.571300 0.000000 + 2 1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 7 + 11 10 + 12 10 + 13 10 + 14 13 + 15 14 + 16 14 + 17 14 + 18 5 + 19 18 diff --git a/src/data/amber_s/MET_N.sgm b/src/data/amber_s/MET_N.sgm new file mode 100644 index 0000000..066b78f --- /dev/null +++ b/src/data/amber_s/MET_N.sgm @@ -0,0 +1,215 @@ +# +$MET_N + 4.600000 + 19 18 32 36 0 0 1 1 + 0.000000 + 1 N 0 0 0 1 1 + N3 0.159200 0.000000 + 22H 0 0 0 1 1 + H 0.198400 0.000000 + 33H 0 0 0 1 1 + H 0.198400 0.000000 + 44H 0 0 0 1 1 + H 0.198400 0.000000 + 5 CA 0 0 0 1 1 + CT 0.022100 0.000000 + 6 HA 0 0 0 1 1 + HP 0.111600 0.000000 + 7 CB 0 0 0 1 1 + CT 0.086500 0.000000 + 82HB 0 0 0 1 1 + HC 0.012500 0.000000 + 93HB 0 0 0 1 1 + HC 0.012500 0.000000 + 10 CG 0 0 0 1 1 + CT 0.033400 0.000000 + 112HG 0 0 0 1 1 + H1 0.029200 0.000000 + 123HG 0 0 0 1 1 + H1 0.029200 0.000000 + 13 SD 0 0 0 1 1 + S -0.277400 0.000000 + 14 CE 0 0 0 1 1 + CT -0.034100 0.000000 + 152HE 0 0 0 1 1 + H1 0.059700 0.000000 + 163HE 0 0 0 1 1 + H1 0.059700 0.000000 + 174HE 0 0 0 1 1 + H1 0.059700 0.000000 + 18 C 2 1 0 1 1 + C 0.612300 0.000000 + 19 O 0 0 0 1 1 + O -0.571300 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 5 6 0 0 + 0.000000 0.00000E+00 + 6 5 7 0 0 + 0.000000 0.00000E+00 + 7 5 18 0 0 + 0.000000 0.00000E+00 + 8 7 8 0 0 + 0.000000 0.00000E+00 + 9 7 9 0 0 + 0.000000 0.00000E+00 + 10 7 10 0 0 + 0.000000 0.00000E+00 + 11 10 11 0 0 + 0.000000 0.00000E+00 + 12 10 12 0 0 + 0.000000 0.00000E+00 + 13 10 13 0 0 + 0.000000 0.00000E+00 + 14 13 14 0 0 + 0.000000 0.00000E+00 + 15 14 15 0 0 + 0.000000 0.00000E+00 + 16 14 16 0 0 + 0.000000 0.00000E+00 + 17 14 17 0 0 + 0.000000 0.00000E+00 + 18 18 19 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 2 1 5 0 0 + 0.000000 0.00000E+00 + 4 3 1 4 0 0 + 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0.000000 0.00000E+00 + 22 5 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 5 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 24 5 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 25 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 26 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 27 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 28 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 29 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 30 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 31 7 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 32 11 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 33 12 10 13 14 0 0 + 0 0.000000 0.00000E+00 + 34 10 13 14 15 0 0 + 0 0.000000 0.00000E+00 + 35 10 13 14 16 0 0 + 0 0.000000 0.00000E+00 + 36 10 13 14 17 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/MG.frg b/src/data/amber_s/MG.frg new file mode 100644 index 0000000..2cc4454 --- /dev/null +++ b/src/data/amber_s/MG.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$MG + 1 1 1 0 +MG + 1Mg Mg 0 0 0 1 1 2.000000 0.000000 diff --git a/src/data/amber_s/NME.frg b/src/data/amber_s/NME.frg new file mode 100644 index 0000000..98f1baf --- /dev/null +++ b/src/data/amber_s/NME.frg @@ -0,0 +1,14 @@ +$NME + 6 1 1 0 +NME + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CH3 CT 0 0 0 1 1 -0.149000 0.000000 + 42HH3 H1 0 0 0 1 1 0.097600 0.000000 + 53HH3 H1 0 0 0 1 1 0.097600 0.000000 + 64HH3 H1 0 0 0 1 1 0.097600 0.000000 + 2 1 + 3 1 + 4 3 + 5 3 + 6 3 diff --git a/src/data/amber_s/NME_C.sgm b/src/data/amber_s/NME_C.sgm new file mode 100644 index 0000000..8364253 --- /dev/null +++ b/src/data/amber_s/NME_C.sgm @@ -0,0 +1,47 @@ +# +$NME_C + 4.600000 + 6 5 7 3 0 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT -0.149000 0.000000 + 42HA 0 0 0 1 1 + H1 0.097600 0.000000 + 53HA 0 0 0 1 1 + H1 0.097600 0.000000 + 64HA 0 0 0 1 1 + H1 0.097600 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 6 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 6 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 6 0 0 + 0.000000 0.00000E+00 + 7 5 3 6 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 6 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/Na.frg b/src/data/amber_s/Na.frg new file mode 100644 index 0000000..1fa649a --- /dev/null +++ b/src/data/amber_s/Na.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$Na + 1 1 1 0 +Na + 1Na Na 0 0 0 1 1 1.000000 0.000000 diff --git a/src/data/amber_s/Na.sgm b/src/data/amber_s/Na.sgm new file mode 100644 index 0000000..a6249ff --- /dev/null +++ b/src/data/amber_s/Na.sgm @@ -0,0 +1,7 @@ +# This is an automatically generated segment file +# + 4.600000 + 1 0 0 0 0 0 1 1 + 0.000000 + 1Na 0 0 0 1 1 + Na 1.000000 0.000000 diff --git a/src/data/amber_s/PHE.frg b/src/data/amber_s/PHE.frg new file mode 100644 index 0000000..091a13d --- /dev/null +++ b/src/data/amber_s/PHE.frg @@ -0,0 +1,31 @@ +$PHE + 20 1 1 0 +PHE + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.002400 0.000000 + 4 HA H1 0 0 0 1 1 0.097800 0.000000 + 5 CB CT 0 0 0 1 1 -0.034300 0.000000 + 62HB HC 0 0 0 1 1 0.029500 0.000000 + 73HB HC 0 0 0 1 1 0.029500 0.000000 + 8 CG CA 0 1 0 1 1 0.011800 0.000000 + 9 CD1 CA 0 1 0 1 1 -0.125600 0.000000 + 10 HD1 HA 0 0 0 1 1 0.133000 0.000000 + 11 CE1 CA 0 1 0 1 1 -0.170400 0.000000 + 12 HE1 HA 0 0 0 1 1 0.143000 0.000000 + 13 CZ CA 0 1 0 1 1 -0.107200 0.000000 + 14 HZ HA 0 0 0 1 1 0.129700 0.000000 + 15 CE2 CA 0 1 0 1 1 -0.170400 0.000000 + 16 HE2 HA 0 0 0 1 1 0.143000 0.000000 + 17 CD2 CA 0 1 0 1 1 -0.125600 0.000000 + 18 HD2 HA 0 0 0 1 1 0.133000 0.000000 + 19 C C 2 1 0 1 1 0.597300 0.000000 + 20 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 3 19 20 + 4 3 5 8 9 11 13 15 17 8 + 6 5 7 + 9 10 + 11 12 + 13 14 + 15 16 + 17 18 diff --git a/src/data/amber_s/PHE.sgm b/src/data/amber_s/PHE.sgm new file mode 100644 index 0000000..e16237b --- /dev/null +++ b/src/data/amber_s/PHE.sgm @@ -0,0 +1,258 @@ +# +$PHE + 4.600000 + 20 20 32 45 6 7 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT -0.002400 0.000000 + 4 HA 0 0 0 1 1 + H1 0.097800 0.000000 + 5 CB 0 0 0 1 1 + CT -0.034300 0.000000 + 62HB 0 0 0 1 1 + HC 0.029500 0.000000 + 73HB 0 0 0 1 1 + HC 0.029500 0.000000 + 8 CG 0 1 0 1 1 + CA 0.011800 0.000000 + 9 CD1 0 1 0 1 1 + CA -0.125600 0.000000 + 10 HD1 0 0 0 1 1 + HA 0.133000 0.000000 + 11 CE1 0 1 0 1 1 + CA -0.170400 0.000000 + 12 HE1 0 0 0 1 1 + HA 0.143000 0.000000 + 13 CZ 0 1 0 1 1 + CA -0.107200 0.000000 + 14 HZ 0 0 0 1 1 + HA 0.129700 0.000000 + 15 CE2 0 1 0 1 1 + CA -0.170400 0.000000 + 16 HE2 0 0 0 1 1 + HA 0.143000 0.000000 + 17 CD2 0 1 0 1 1 + CA -0.125600 0.000000 + 18 HD2 0 0 0 1 1 + HA 0.133000 0.000000 + 19 C 2 1 0 1 1 + C 0.597300 0.000000 + 20 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 19 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 8 17 0 0 + 0.000000 0.00000E+00 + 11 9 10 0 0 + 0.000000 0.00000E+00 + 12 9 11 0 0 + 0.000000 0.00000E+00 + 13 11 12 0 0 + 0.000000 0.00000E+00 + 14 11 13 0 0 + 0.000000 0.00000E+00 + 15 13 14 0 0 + 0.000000 0.00000E+00 + 16 13 15 0 0 + 0.000000 0.00000E+00 + 17 15 16 0 0 + 0.000000 0.00000E+00 + 18 15 17 0 0 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0.000000 + 1 11 13 14 + 13 15 + 1 2 5 8 11 + 11 12 + 3 2 4 + 6 5 7 + 9 8 10 diff --git a/src/data/amber_s/PRO_C.sgm b/src/data/amber_s/PRO_C.sgm new file mode 100644 index 0000000..66cbc5a --- /dev/null +++ b/src/data/amber_s/PRO_C.sgm @@ -0,0 +1,203 @@ +# +$PRO_C + 4.600000 + 15 15 28 39 2 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.280200 0.000000 + 2 CA 0 0 0 1 1 + CT -0.133600 0.000000 + 3 HA 0 0 0 1 1 + H1 0.077600 0.000000 + 4 CB 0 0 0 1 1 + CT -0.054300 0.000000 + 52HB 0 0 0 1 1 + HC 0.038100 0.000000 + 63HB 0 0 0 1 1 + HC 0.038100 0.000000 + 7 CG 0 0 0 1 1 + CT 0.046600 0.000000 + 82HG 0 0 0 1 1 + HC 0.017200 0.000000 + 93HG 0 0 0 1 1 + HC 0.017200 0.000000 + 10 CD 0 0 0 1 1 + CT 0.043400 0.000000 + 112HD 0 0 0 1 1 + H1 0.033100 0.000000 + 123HD 0 0 0 1 1 + H1 0.033100 0.000000 + 13 C 0 1 0 1 1 + C 0.663100 0.000000 + 14 O 0 0 0 1 1 + O2 -0.769700 0.000000 + 15 OXT 0 0 0 1 1 + O2 -0.769700 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 10 0 0 + 0.000000 0.00000E+00 + 3 2 3 0 0 + 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0000000..150a439 --- /dev/null +++ b/src/data/amber_s/RA.frg @@ -0,0 +1,72 @@ +#R-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group +$RA + 33 1 1 0 +R-ADEN + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.039400 0.000000 + 12 H1* H2 0 0 0 1 1 0.200700 0.000000 + 13 N9 N* 0 1 0 1 1 -0.025100 0.000000 + 14 C8 CK 0 1 0 1 1 0.200600 0.000000 + 15 H8 H5 0 0 0 1 1 0.155300 0.000000 + 16 N7 NB 0 0 0 1 1 -0.607300 0.000000 + 17 C5 CB 0 0 0 1 1 0.051500 0.000000 + 18 C6 CA 0 1 0 1 1 0.700900 0.000000 + 19 N6 N2 0 1 0 1 1 -0.901900 0.000000 + 202H6 H 0 0 0 1 1 0.411500 0.000000 + 213H6 H 0 0 0 1 1 0.411500 0.000000 + 22 N1 NC 0 0 0 1 1 -0.761500 0.000000 + 23 C2 CQ 0 1 0 1 1 0.587500 0.000000 + 24 H2 H5 0 0 0 1 1 0.047300 0.000000 + 25 N3 NC 0 0 0 1 1 -0.699700 0.000000 + 26 C4 CB 0 0 0 1 1 0.305300 0.000000 + 27 C3* CT 0 0 0 1 1 0.202200 0.000000 + 28 H3* H1 0 0 0 1 1 0.061500 0.000000 + 29 C2* CT 0 0 0 1 1 0.067000 0.000000 + 302H2* H1 0 0 0 1 1 0.097200 0.000000 + 31 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 323HO* HO 0 0 0 1 1 0.418600 0.000000 + 33 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 23 25 + 25 26 + 8 27 + 27 28 + 27 29 + 29 30 + 29 31 + 31 32 + 27 33 + 11 29 + 17 26 + 13 26 diff --git a/src/data/amber_s/RA_3.frg b/src/data/amber_s/RA_3.frg new file mode 100644 index 0000000..18e5185 --- /dev/null +++ b/src/data/amber_s/RA_3.frg @@ -0,0 +1,74 @@ +#R-ADENOSINE - with 5' - phosphate group and 3' - OH group +$RA3 + 34 1 1 0 +R-ADEN + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.039400 0.000000 + 12 H1* H2 0 0 0 1 1 0.200700 0.000000 + 13 N9 N* 0 1 0 1 1 -0.025100 0.000000 + 14 C8 CK 0 1 0 1 1 0.200600 0.000000 + 15 H8 H5 0 0 0 1 1 0.155300 0.000000 + 16 N7 NB 0 0 0 1 1 -0.607300 0.000000 + 17 C5 CB 0 0 0 1 1 0.051500 0.000000 + 18 C6 CA 0 1 0 1 1 0.700900 0.000000 + 19 N6 N2 0 1 0 1 1 -0.901900 0.000000 + 202H6 H 0 0 0 1 1 0.411500 0.000000 + 213H6 H 0 0 0 1 1 0.411500 0.000000 + 22 N1 NC 0 0 0 1 1 -0.761500 0.000000 + 23 C2 CQ 0 1 0 1 1 0.587500 0.000000 + 24 H2 H5 0 0 0 1 1 0.047300 0.000000 + 25 N3 NC 0 0 0 1 1 -0.699700 0.000000 + 26 C4 CB 0 0 0 1 1 0.305300 0.000000 + 27 C3* CT 0 0 0 1 1 0.202200 0.000000 + 28 H3* H1 0 0 0 1 1 0.061500 0.000000 + 29 C2* CT 0 0 0 1 1 0.067000 0.000000 + 302H2* H1 0 0 0 1 1 0.097200 0.000000 + 31 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 323HO* HO 0 0 0 1 1 0.418600 0.000000 + 33 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 34 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 23 25 + 25 26 + 8 27 + 27 28 + 27 29 + 29 30 + 29 31 + 31 32 + 27 33 + 33 34 + 11 29 + 17 26 + 13 26 diff --git a/src/data/amber_s/RA_5.frg b/src/data/amber_s/RA_5.frg new file mode 100644 index 0000000..c341406 --- /dev/null +++ b/src/data/amber_s/RA_5.frg @@ -0,0 +1,68 @@ +#R-ADENOSINE - with 5' - OH end group and 3' - O(minus) +$RA5 + 31 1 1 0 +R-ADEN + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.039400 0.000000 + 10 H1* H2 0 0 0 1 1 0.200700 0.000000 + 11 N9 N* 0 1 0 1 1 -0.025100 0.000000 + 12 C8 CK 0 1 0 1 1 0.200600 0.000000 + 13 H8 H5 0 0 0 1 1 0.155300 0.000000 + 14 N7 NB 0 0 0 1 1 -0.607300 0.000000 + 15 C5 CB 0 0 0 1 1 0.051500 0.000000 + 16 C6 CA 0 1 0 1 1 0.700900 0.000000 + 17 N6 N2 0 1 0 1 1 -0.901900 0.000000 + 182H6 H 0 0 0 1 1 0.411500 0.000000 + 193H6 H 0 0 0 1 1 0.411500 0.000000 + 20 N1 NC 0 0 0 1 1 -0.761500 0.000000 + 21 C2 CQ 0 1 0 1 1 0.587500 0.000000 + 22 H2 H5 0 0 0 1 1 0.047300 0.000000 + 23 N3 NC 0 0 0 1 1 -0.699700 0.000000 + 24 C4 CB 0 0 0 1 1 0.305300 0.000000 + 25 C3* CT 0 0 0 1 1 0.202200 0.000000 + 26 H3* H1 0 0 0 1 1 0.061500 0.000000 + 27 C2* CT 0 0 0 1 1 0.067000 0.000000 + 282H2* H1 0 0 0 1 1 0.097200 0.000000 + 29 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 303HO* HO 0 0 0 1 1 0.418600 0.000000 + 31 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 21 23 + 23 24 + 6 25 + 25 26 + 25 27 + 27 28 + 27 29 + 29 30 + 25 31 + 9 27 + 15 24 + 11 24 diff --git a/src/data/amber_s/RA_M.frg b/src/data/amber_s/RA_M.frg new file mode 100644 index 0000000..c40943a --- /dev/null +++ b/src/data/amber_s/RA_M.frg @@ -0,0 +1,70 @@ +#R-ADENOSINE - with 5' - OH group and 3' - OH group +$RAN + 32 1 1 0 +R-ADEN + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.039400 0.000000 + 10 H1* H2 0 0 0 1 1 0.200700 0.000000 + 11 N9 N* 0 1 0 1 1 -0.025100 0.000000 + 12 C8 CK 0 1 0 1 1 0.200600 0.000000 + 13 H8 H5 0 0 0 1 1 0.155300 0.000000 + 14 N7 NB 0 0 0 1 1 -0.607300 0.000000 + 15 C5 CB 0 0 0 1 1 0.051500 0.000000 + 16 C6 CA 0 1 0 1 1 0.700900 0.000000 + 17 N6 N2 0 1 0 1 1 -0.901900 0.000000 + 182H6 H 0 0 0 1 1 0.411500 0.000000 + 193H6 H 0 0 0 1 1 0.411500 0.000000 + 20 N1 NC 0 0 0 1 1 -0.761500 0.000000 + 21 C2 CQ 0 1 0 1 1 0.587500 0.000000 + 22 H2 H5 0 0 0 1 1 0.047300 0.000000 + 23 N3 NC 0 0 0 1 1 -0.699700 0.000000 + 24 C4 CB 0 0 0 1 1 0.305300 0.000000 + 25 C3* CT 0 0 0 1 1 0.202200 0.000000 + 26 H3* H1 0 0 0 1 1 0.061500 0.000000 + 27 C2* CT 0 0 0 1 1 0.067000 0.000000 + 282H2* H1 0 0 0 1 1 0.097200 0.000000 + 29 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 303HO* HO 0 0 0 1 1 0.418600 0.000000 + 31 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 32 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 21 23 + 23 24 + 6 25 + 25 26 + 25 27 + 27 28 + 27 29 + 29 30 + 25 31 + 31 32 + 9 27 + 15 24 + 11 24 diff --git a/src/data/amber_s/RC.frg b/src/data/amber_s/RC.frg new file mode 100644 index 0000000..3bee3cd --- /dev/null +++ b/src/data/amber_s/RC.frg @@ -0,0 +1,67 @@ +#R-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group +$RC + 31 1 1 0 +R-CYTO + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.006600 0.000000 + 12 H1* H2 0 0 0 1 1 0.202900 0.000000 + 13 N1 N* 0 1 0 1 1 -0.048400 0.000000 + 14 C6 CM 0 1 0 1 1 0.005300 0.000000 + 15 H6 H4 0 0 0 1 1 0.195800 0.000000 + 16 C5 CM 0 1 0 1 1 -0.521500 0.000000 + 17 H5 HA 0 0 0 1 1 0.192800 0.000000 + 18 C4 CA 0 1 0 1 1 0.818500 0.000000 + 19 N4 N2 0 1 0 1 1 -0.953000 0.000000 + 202H4 H 0 0 0 1 1 0.423400 0.000000 + 213H4 H 0 0 0 1 1 0.423400 0.000000 + 22 N3 NC 0 0 0 1 1 -0.758400 0.000000 + 23 C2 C 0 1 0 1 1 0.753800 0.000000 + 24 O2 O 0 0 0 1 1 -0.625200 0.000000 + 25 C3* CT 0 0 0 1 1 0.202200 0.000000 + 26 H3* H1 0 0 0 1 1 0.061500 0.000000 + 27 C2* CT 0 0 0 1 1 0.067000 0.000000 + 282H2* H1 0 0 0 1 1 0.097200 0.000000 + 29 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 303HO* HO 0 0 0 1 1 0.418600 0.000000 + 31 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 8 25 + 25 26 + 25 27 + 27 28 + 27 29 + 29 30 + 25 31 + 11 27 + 13 23 diff --git a/src/data/amber_s/RC_3.frg b/src/data/amber_s/RC_3.frg new file mode 100644 index 0000000..ff42869 --- /dev/null +++ b/src/data/amber_s/RC_3.frg @@ -0,0 +1,69 @@ +#R-CYTOSINE - with 5' - phosphate group and 3' - OH group +$RC3 + 32 1 1 0 +R-CYTO + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.006600 0.000000 + 12 H1* H2 0 0 0 1 1 0.202900 0.000000 + 13 N1 N* 0 1 0 1 1 -0.048400 0.000000 + 14 C6 CM 0 1 0 1 1 0.005300 0.000000 + 15 H6 H4 0 0 0 1 1 0.195800 0.000000 + 16 C5 CM 0 1 0 1 1 -0.521500 0.000000 + 17 H5 HA 0 0 0 1 1 0.192800 0.000000 + 18 C4 CA 0 1 0 1 1 0.818500 0.000000 + 19 N4 N2 0 1 0 1 1 -0.953000 0.000000 + 202H4 H 0 0 0 1 1 0.423400 0.000000 + 213H4 H 0 0 0 1 1 0.423400 0.000000 + 22 N3 NC 0 0 0 1 1 -0.758400 0.000000 + 23 C2 C 0 1 0 1 1 0.753800 0.000000 + 24 O2 O 0 0 0 1 1 -0.625200 0.000000 + 25 C3* CT 0 0 0 1 1 0.202200 0.000000 + 26 H3* H1 0 0 0 1 1 0.061500 0.000000 + 27 C2* CT 0 0 0 1 1 0.067000 0.000000 + 282H2* H1 0 0 0 1 1 0.097200 0.000000 + 29 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 303HO* HO 0 0 0 1 1 0.418600 0.000000 + 31 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 32 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 19 20 + 19 21 + 18 22 + 22 23 + 23 24 + 8 25 + 25 26 + 25 27 + 27 28 + 27 29 + 29 30 + 25 31 + 31 32 + 11 27 + 13 23 diff --git a/src/data/amber_s/RC_5.frg b/src/data/amber_s/RC_5.frg new file mode 100644 index 0000000..d898bf2 --- /dev/null +++ b/src/data/amber_s/RC_5.frg @@ -0,0 +1,63 @@ +#R-CYTOSINE - with 5' - OH end group and 3' - O(minus) group +$RC5 + 29 1 1 0 +R-CYTO + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.006600 0.000000 + 10 H1* H2 0 0 0 1 1 0.202900 0.000000 + 11 N1 N* 0 1 0 1 1 -0.048400 0.000000 + 12 C6 CM 0 1 0 1 1 0.005300 0.000000 + 13 H6 H4 0 0 0 1 1 0.195800 0.000000 + 14 C5 CM 0 1 0 1 1 -0.521500 0.000000 + 15 H5 HA 0 0 0 1 1 0.192800 0.000000 + 16 C4 CA 0 1 0 1 1 0.818500 0.000000 + 17 N4 N2 0 1 0 1 1 -0.953000 0.000000 + 182H4 H 0 0 0 1 1 0.423400 0.000000 + 193H4 H 0 0 0 1 1 0.423400 0.000000 + 20 N3 NC 0 0 0 1 1 -0.758400 0.000000 + 21 C2 C 0 1 0 1 1 0.753800 0.000000 + 22 O2 O 0 0 0 1 1 -0.625200 0.000000 + 23 C3* CT 0 0 0 1 1 0.202200 0.000000 + 24 H3* H1 0 0 0 1 1 0.061500 0.000000 + 25 C2* CT 0 0 0 1 1 0.067000 0.000000 + 262H2* H1 0 0 0 1 1 0.097200 0.000000 + 27 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 283HO* HO 0 0 0 1 1 0.418600 0.000000 + 29 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 6 23 + 23 24 + 23 25 + 25 26 + 25 27 + 27 28 + 23 29 + 9 25 + 11 21 diff --git a/src/data/amber_s/RC_M.frg b/src/data/amber_s/RC_M.frg new file mode 100644 index 0000000..4b448c4 --- /dev/null +++ b/src/data/amber_s/RC_M.frg @@ -0,0 +1,65 @@ +#R-CYTOSINE - with 5' - OH group and 3' - OH group +$RCN + 30 1 1 0 +R-CYTO + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.006600 0.000000 + 10 H1* H2 0 0 0 1 1 0.202900 0.000000 + 11 N1 N* 0 1 0 1 1 -0.048400 0.000000 + 12 C6 CM 0 1 0 1 1 0.005300 0.000000 + 13 H6 H4 0 0 0 1 1 0.195800 0.000000 + 14 C5 CM 0 1 0 1 1 -0.521500 0.000000 + 15 H5 HA 0 0 0 1 1 0.192800 0.000000 + 16 C4 CA 0 1 0 1 1 0.818500 0.000000 + 17 N4 N2 0 1 0 1 1 -0.953000 0.000000 + 182H4 H 0 0 0 1 1 0.423400 0.000000 + 193H4 H 0 0 0 1 1 0.423400 0.000000 + 20 N3 NC 0 0 0 1 1 -0.758400 0.000000 + 21 C2 C 0 1 0 1 1 0.753800 0.000000 + 22 O2 O 0 0 0 1 1 -0.625200 0.000000 + 23 C3* CT 0 0 0 1 1 0.202200 0.000000 + 24 H3* H1 0 0 0 1 1 0.061500 0.000000 + 25 C2* CT 0 0 0 1 1 0.067000 0.000000 + 262H2* H1 0 0 0 1 1 0.097200 0.000000 + 27 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 283HO* HO 0 0 0 1 1 0.418600 0.000000 + 29 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 30 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 17 18 + 17 19 + 16 20 + 20 21 + 21 22 + 6 23 + 23 24 + 23 25 + 25 26 + 25 27 + 27 28 + 23 29 + 29 30 + 9 25 + 11 21 diff --git a/src/data/amber_s/RG.frg b/src/data/amber_s/RG.frg new file mode 100644 index 0000000..f82ac1a --- /dev/null +++ b/src/data/amber_s/RG.frg @@ -0,0 +1,74 @@ +#R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group +$RG + 34 1 1 0 +R-GUAN + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.019100 0.000000 + 12 H1* H2 0 0 0 1 1 0.200600 0.000000 + 13 N9 N* 0 1 0 1 1 0.049200 0.000000 + 14 C8 CK 0 1 0 1 1 0.137400 0.000000 + 15 H8 H5 0 0 0 1 1 0.164000 0.000000 + 16 N7 NB 0 0 0 1 1 -0.570900 0.000000 + 17 C5 CB 0 0 0 1 1 0.174400 0.000000 + 18 C6 C 0 1 0 1 1 0.477000 0.000000 + 19 O6 O 0 0 0 1 1 -0.559700 0.000000 + 20 N1 NA 0 1 0 1 1 -0.478700 0.000000 + 21 H1 H 0 0 0 1 1 0.342400 0.000000 + 22 C2 CA 0 1 0 1 1 0.765700 0.000000 + 23 N2 N2 0 1 0 1 1 -0.967200 0.000000 + 242H2 H 0 0 0 1 1 0.436400 0.000000 + 253H2 H 0 0 0 1 1 0.436400 0.000000 + 26 N3 NC 0 0 0 1 1 -0.632300 0.000000 + 27 C4 CB 0 0 0 1 1 0.122200 0.000000 + 28 C3* CT 0 0 0 1 1 0.202200 0.000000 + 29 H3* H1 0 0 0 1 1 0.061500 0.000000 + 30 C2* CT 0 0 0 1 1 0.067000 0.000000 + 312H2* H1 0 0 0 1 1 0.097200 0.000000 + 32 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 333HO* HO 0 0 0 1 1 0.418600 0.000000 + 34 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 18 20 + 20 21 + 20 22 + 22 23 + 23 24 + 23 25 + 22 26 + 26 27 + 8 28 + 28 29 + 28 30 + 30 31 + 30 32 + 32 33 + 28 34 + 11 30 + 17 27 + 13 27 diff --git a/src/data/amber_s/RG_3.frg b/src/data/amber_s/RG_3.frg new file mode 100644 index 0000000..fe74815 --- /dev/null +++ b/src/data/amber_s/RG_3.frg @@ -0,0 +1,76 @@ +#R-GUANOSINE - with 5' - phosphate group and 3' - OH group +$RG3 + 35 1 1 0 +R-GUAN + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.019100 0.000000 + 12 H1* H2 0 0 0 1 1 0.200600 0.000000 + 13 N9 N* 0 1 0 1 1 0.049200 0.000000 + 14 C8 CK 0 1 0 1 1 0.137400 0.000000 + 15 H8 H5 0 0 0 1 1 0.164000 0.000000 + 16 N7 NB 0 0 0 1 1 -0.570900 0.000000 + 17 C5 CB 0 0 0 1 1 0.174400 0.000000 + 18 C6 C 0 1 0 1 1 0.477000 0.000000 + 19 O6 O 0 0 0 1 1 -0.559700 0.000000 + 20 N1 NA 0 1 0 1 1 -0.478700 0.000000 + 21 H1 H 0 0 0 1 1 0.342400 0.000000 + 22 C2 CA 0 1 0 1 1 0.765700 0.000000 + 23 N2 N2 0 1 0 1 1 -0.967200 0.000000 + 242H2 H 0 0 0 1 1 0.436400 0.000000 + 253H2 H 0 0 0 1 1 0.436400 0.000000 + 26 N3 NC 0 0 0 1 1 -0.632300 0.000000 + 27 C4 CB 0 0 0 1 1 0.122200 0.000000 + 28 C3* CT 0 0 0 1 1 0.202200 0.000000 + 29 H3* H1 0 0 0 1 1 0.061500 0.000000 + 30 C2* CT 0 0 0 1 1 0.067000 0.000000 + 312H2* H1 0 0 0 1 1 0.097200 0.000000 + 32 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 333HO* HO 0 0 0 1 1 0.418600 0.000000 + 34 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 35 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 17 18 + 18 19 + 18 20 + 20 21 + 20 22 + 22 23 + 23 24 + 23 25 + 22 26 + 26 27 + 8 28 + 28 29 + 28 30 + 30 31 + 30 32 + 32 33 + 28 34 + 34 35 + 11 30 + 17 27 + 13 27 diff --git a/src/data/amber_s/RG_5.frg b/src/data/amber_s/RG_5.frg new file mode 100644 index 0000000..f15560e --- /dev/null +++ b/src/data/amber_s/RG_5.frg @@ -0,0 +1,70 @@ +#R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group +$RG5 + 32 1 1 0 +R-GUAN + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.019100 0.000000 + 10 H1* H2 0 0 0 1 1 0.200600 0.000000 + 11 N9 N* 0 1 0 1 1 0.049200 0.000000 + 12 C8 CK 0 1 0 1 1 0.137400 0.000000 + 13 H8 H5 0 0 0 1 1 0.164000 0.000000 + 14 N7 NB 0 0 0 1 1 -0.570900 0.000000 + 15 C5 CB 0 0 0 1 1 0.174400 0.000000 + 16 C6 C 0 1 0 1 1 0.477000 0.000000 + 17 O6 O 0 0 0 1 1 -0.559700 0.000000 + 18 N1 NA 0 1 0 1 1 -0.478700 0.000000 + 19 H1 H 0 0 0 1 1 0.342400 0.000000 + 20 C2 CA 0 1 0 1 1 0.765700 0.000000 + 21 N2 N2 0 1 0 1 1 -0.967200 0.000000 + 222H2 H 0 0 0 1 1 0.436400 0.000000 + 233H2 H 0 0 0 1 1 0.436400 0.000000 + 24 N3 NC 0 0 0 1 1 -0.632300 0.000000 + 25 C4 CB 0 0 0 1 1 0.122200 0.000000 + 26 C3* CT 0 0 0 1 1 0.202200 0.000000 + 27 H3* H1 0 0 0 1 1 0.061500 0.000000 + 28 C2* CT 0 0 0 1 1 0.067000 0.000000 + 292H2* H1 0 0 0 1 1 0.097200 0.000000 + 30 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 313HO* HO 0 0 0 1 1 0.418600 0.000000 + 32 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 21 22 + 21 23 + 20 24 + 24 25 + 6 26 + 26 27 + 26 28 + 28 29 + 28 30 + 30 31 + 26 32 + 9 28 + 15 25 + 11 25 diff --git a/src/data/amber_s/RG_M.frg b/src/data/amber_s/RG_M.frg new file mode 100644 index 0000000..251003e --- /dev/null +++ b/src/data/amber_s/RG_M.frg @@ -0,0 +1,72 @@ +#R-GUANOSINE - with 5' - OH group and 3' - OH group +$RGN + 33 1 1 0 +R-GUAN + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.019100 0.000000 + 10 H1* H2 0 0 0 1 1 0.200600 0.000000 + 11 N9 N* 0 1 0 1 1 0.049200 0.000000 + 12 C8 CK 0 1 0 1 1 0.137400 0.000000 + 13 H8 H5 0 0 0 1 1 0.164000 0.000000 + 14 N7 NB 0 0 0 1 1 -0.570900 0.000000 + 15 C5 CB 0 0 0 1 1 0.174400 0.000000 + 16 C6 C 0 1 0 1 1 0.477000 0.000000 + 17 O6 O 0 0 0 1 1 -0.559700 0.000000 + 18 N1 NA 0 1 0 1 1 -0.478700 0.000000 + 19 H1 H 0 0 0 1 1 0.342400 0.000000 + 20 C2 CA 0 1 0 1 1 0.765700 0.000000 + 21 N2 N2 0 1 0 1 1 -0.967200 0.000000 + 222H2 H 0 0 0 1 1 0.436400 0.000000 + 233H2 H 0 0 0 1 1 0.436400 0.000000 + 24 N3 NC 0 0 0 1 1 -0.632300 0.000000 + 25 C4 CB 0 0 0 1 1 0.122200 0.000000 + 26 C3* CT 0 0 0 1 1 0.202200 0.000000 + 27 H3* H1 0 0 0 1 1 0.061500 0.000000 + 28 C2* CT 0 0 0 1 1 0.067000 0.000000 + 292H2* H1 0 0 0 1 1 0.097200 0.000000 + 30 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 313HO* HO 0 0 0 1 1 0.418600 0.000000 + 32 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 33 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 15 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 21 22 + 21 23 + 20 24 + 24 25 + 6 26 + 26 27 + 26 28 + 28 29 + 28 30 + 30 31 + 26 32 + 32 33 + 9 28 + 15 25 + 11 25 diff --git a/src/data/amber_s/RU.frg b/src/data/amber_s/RU.frg new file mode 100644 index 0000000..1d07355 --- /dev/null +++ b/src/data/amber_s/RU.frg @@ -0,0 +1,65 @@ +#R-URACIL - with 5' - phosphate group and 3' - O(minus) group +$RU + 30 1 1 0 +R-URAC + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.067400 0.000000 + 12 H1* H2 0 0 0 1 1 0.182400 0.000000 + 13 N1 N* 0 1 0 1 1 0.041800 0.000000 + 14 C6 CM 0 1 0 1 1 -0.112600 0.000000 + 15 H6 H4 0 0 0 1 1 0.218800 0.000000 + 16 C5 CM 0 1 0 1 1 -0.363500 0.000000 + 17 H5 HA 0 0 0 1 1 0.181100 0.000000 + 18 C4 C 0 1 0 1 1 0.595200 0.000000 + 19 O4 O 0 0 0 1 1 -0.576100 0.000000 + 20 N3 NA 0 1 0 1 1 -0.354900 0.000000 + 21 H3 H 0 0 0 1 1 0.315400 0.000000 + 22 C2 C 0 1 0 1 1 0.468700 0.000000 + 23 O2 O 0 0 0 1 1 -0.547700 0.000000 + 24 C3* CT 0 0 0 1 1 0.202200 0.000000 + 25 H3* H1 0 0 0 1 1 0.061500 0.000000 + 26 C2* CT 0 0 0 1 1 0.067000 0.000000 + 272H2* H1 0 0 0 1 1 0.097200 0.000000 + 28 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 293HO* HO 0 0 0 1 1 0.418600 0.000000 + 30 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 20 22 + 22 23 + 8 24 + 24 25 + 24 26 + 26 27 + 26 28 + 28 29 + 24 30 + 11 26 + 13 22 diff --git a/src/data/amber_s/RU_3.frg b/src/data/amber_s/RU_3.frg new file mode 100644 index 0000000..84cb6b6 --- /dev/null +++ b/src/data/amber_s/RU_3.frg @@ -0,0 +1,67 @@ +#R-URACIL - with 5' - phosphate group and 3' - OH group +$RU3 + 31 1 1 0 +R-URAC + 1 P P 3 0 0 1 1 1.166200 0.000000 + 2 O1P O2 0 0 0 1 1 -0.776000 0.000000 + 3 O2P O2 0 0 0 1 1 -0.776000 0.000000 + 4 O5* OS 0 0 0 1 1 -0.498900 0.000000 + 5 C5* CT 0 0 0 1 1 0.055800 0.000000 + 62H5* H1 0 0 0 1 1 0.067900 0.000000 + 73H5* H1 0 0 0 1 1 0.067900 0.000000 + 8 C4* CT 0 0 0 1 1 0.106500 0.000000 + 9 H4* H1 0 0 0 1 1 0.117400 0.000000 + 10 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 11 C1* CT 0 0 0 1 1 0.067400 0.000000 + 12 H1* H2 0 0 0 1 1 0.182400 0.000000 + 13 N1 N* 0 1 0 1 1 0.041800 0.000000 + 14 C6 CM 0 1 0 1 1 -0.112600 0.000000 + 15 H6 H4 0 0 0 1 1 0.218800 0.000000 + 16 C5 CM 0 1 0 1 1 -0.363500 0.000000 + 17 H5 HA 0 0 0 1 1 0.181100 0.000000 + 18 C4 C 0 1 0 1 1 0.595200 0.000000 + 19 O4 O 0 0 0 1 1 -0.576100 0.000000 + 20 N3 NA 0 1 0 1 1 -0.354900 0.000000 + 21 H3 H 0 0 0 1 1 0.315400 0.000000 + 22 C2 C 0 1 0 1 1 0.468700 0.000000 + 23 O2 O 0 0 0 1 1 -0.547700 0.000000 + 24 C3* CT 0 0 0 1 1 0.202200 0.000000 + 25 H3* H1 0 0 0 1 1 0.061500 0.000000 + 26 C2* CT 0 0 0 1 1 0.067000 0.000000 + 272H2* H1 0 0 0 1 1 0.097200 0.000000 + 28 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 293HO* HO 0 0 0 1 1 0.418600 0.000000 + 30 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 31 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 20 22 + 22 23 + 8 24 + 24 25 + 24 26 + 26 27 + 26 28 + 28 29 + 24 30 + 30 31 + 11 26 + 13 22 diff --git a/src/data/amber_s/RU_5.frg b/src/data/amber_s/RU_5.frg new file mode 100644 index 0000000..c9dd724 --- /dev/null +++ b/src/data/amber_s/RU_5.frg @@ -0,0 +1,61 @@ +#R-URACIL - with 5' - OH end group and 3' - O(minus) +$RU5 + 28 1 1 0 +R-URAC + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.067400 0.000000 + 10 H1* H2 0 0 0 1 1 0.182400 0.000000 + 11 N1 N* 0 1 0 1 1 0.041800 0.000000 + 12 C6 CM 0 1 0 1 1 -0.112600 0.000000 + 13 H6 H4 0 0 0 1 1 0.218800 0.000000 + 14 C5 CM 0 1 0 1 1 -0.363500 0.000000 + 15 H5 HA 0 0 0 1 1 0.181100 0.000000 + 16 C4 C 0 1 0 1 1 0.595200 0.000000 + 17 O4 O 0 0 0 1 1 -0.576100 0.000000 + 18 N3 NA 0 1 0 1 1 -0.354900 0.000000 + 19 H3 H 0 0 0 1 1 0.315400 0.000000 + 20 C2 C 0 1 0 1 1 0.468700 0.000000 + 21 O2 O 0 0 0 1 1 -0.547700 0.000000 + 22 C3* CT 0 0 0 1 1 0.202200 0.000000 + 23 H3* H1 0 0 0 1 1 0.061500 0.000000 + 24 C2* CT 0 0 0 1 1 0.067000 0.000000 + 252H2* H1 0 0 0 1 1 0.097200 0.000000 + 26 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 273HO* HO 0 0 0 1 1 0.418600 0.000000 + 28 O3* OS 3 0 0 1 1 -0.524600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 6 22 + 22 23 + 22 24 + 24 25 + 24 26 + 26 27 + 22 28 + 9 24 + 11 20 diff --git a/src/data/amber_s/RU_M.frg b/src/data/amber_s/RU_M.frg new file mode 100644 index 0000000..b08dcac --- /dev/null +++ b/src/data/amber_s/RU_M.frg @@ -0,0 +1,63 @@ +#R-URACIL - with 5' - OH group and 3' - OH group +$RUN + 29 1 1 0 +R-URAC + 1 H5T HO 0 0 0 1 1 0.429500 0.000000 + 2 O5* OH 0 0 0 1 1 -0.622300 0.000000 + 3 C5* CT 0 0 0 1 1 0.055800 0.000000 + 42H5* H1 0 0 0 1 1 0.067900 0.000000 + 53H5* H1 0 0 0 1 1 0.067900 0.000000 + 6 C4* CT 0 0 0 1 1 0.106500 0.000000 + 7 H4* H1 0 0 0 1 1 0.117400 0.000000 + 8 O4* OS 0 0 0 1 1 -0.354800 0.000000 + 9 C1* CT 0 0 0 1 1 0.067400 0.000000 + 10 H1* H2 0 0 0 1 1 0.182400 0.000000 + 11 N1 N* 0 1 0 1 1 0.041800 0.000000 + 12 C6 CM 0 1 0 1 1 -0.112600 0.000000 + 13 H6 H4 0 0 0 1 1 0.218800 0.000000 + 14 C5 CM 0 1 0 1 1 -0.363500 0.000000 + 15 H5 HA 0 0 0 1 1 0.181100 0.000000 + 16 C4 C 0 1 0 1 1 0.595200 0.000000 + 17 O4 O 0 0 0 1 1 -0.576100 0.000000 + 18 N3 NA 0 1 0 1 1 -0.354900 0.000000 + 19 H3 H 0 0 0 1 1 0.315400 0.000000 + 20 C2 C 0 1 0 1 1 0.468700 0.000000 + 21 O2 O 0 0 0 1 1 -0.547700 0.000000 + 22 C3* CT 0 0 0 1 1 0.202200 0.000000 + 23 H3* H1 0 0 0 1 1 0.061500 0.000000 + 24 C2* CT 0 0 0 1 1 0.067000 0.000000 + 252H2* H1 0 0 0 1 1 0.097200 0.000000 + 26 O2* OH 0 0 0 1 1 -0.613900 0.000000 + 273HO* HO 0 0 0 1 1 0.418600 0.000000 + 28 O3* OH 0 0 0 1 1 -0.654100 0.000000 + 29 H3T HO 0 0 0 1 1 0.437600 0.000000 + 1 2 + 2 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 8 9 + 9 10 + 9 11 + 11 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 16 18 + 18 19 + 18 20 + 20 21 + 6 22 + 22 23 + 22 24 + 24 25 + 24 26 + 26 27 + 22 28 + 28 29 + 9 24 + 11 20 diff --git a/src/data/amber_s/SER.frg b/src/data/amber_s/SER.frg new file mode 100644 index 0000000..94610fb --- /dev/null +++ b/src/data/amber_s/SER.frg @@ -0,0 +1,17 @@ +$SER + 11 1 1 0 +SER + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.024900 0.000000 + 4 HA H1 0 0 0 1 1 0.084300 0.000000 + 5 CB CT 0 0 0 1 1 0.211700 0.000000 + 62HB H1 0 0 0 1 1 0.035200 0.000000 + 73HB H1 0 0 0 1 1 0.035200 0.000000 + 8 OG OH 0 0 0 1 1 -0.654600 0.000000 + 9 HG HO 0 0 0 1 1 0.427500 0.000000 + 10 C C 2 1 0 1 1 0.597300 0.000000 + 11 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 3 10 11 + 4 3 5 8 9 + 6 5 7 diff --git a/src/data/amber_s/SER.sgm b/src/data/amber_s/SER.sgm new file mode 100644 index 0000000..13aebb2 --- /dev/null +++ b/src/data/amber_s/SER.sgm @@ -0,0 +1,114 @@ +# +$SER + 4.600000 + 11 10 15 18 0 1 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT -0.024900 0.000000 + 4 HA 0 0 0 1 1 + H1 0.084300 0.000000 + 5 CB 0 0 0 1 1 + CT 0.211700 0.000000 + 62HB 0 0 0 1 1 + H1 0.035200 0.000000 + 73HB 0 0 0 1 1 + H1 0.035200 0.000000 + 8 OG 0 0 0 1 1 + OH -0.654600 0.000000 + 9 HG 0 0 0 1 1 + HO 0.427500 0.000000 + 10 C 2 1 0 1 1 + C 0.597300 0.000000 + 11 O 0 0 0 1 1 + O -0.567900 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 10 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 10 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 10 0 0 + 0.000000 0.00000E+00 + 7 5 3 10 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 7 0 0 + 0.000000 0.00000E+00 + 10 3 5 8 0 0 + 0.000000 0.00000E+00 + 11 6 5 7 0 0 + 0.000000 0.00000E+00 + 12 6 5 8 0 0 + 0.000000 0.00000E+00 + 13 7 5 8 0 0 + 0.000000 0.00000E+00 + 14 5 8 9 0 0 + 0.000000 0.00000E+00 + 15 3 10 11 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 4 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 3 5 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 3 10 0 0 + 0 0.000000 0.00000E+00 + 4 1 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 5 1 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 6 1 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 7 4 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 8 4 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 9 4 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 10 10 3 5 6 0 0 + 0 0.000000 0.00000E+00 + 11 10 3 5 7 0 0 + 0 0.000000 0.00000E+00 + 12 10 3 5 8 0 0 + 0 0.000000 0.00000E+00 + 13 1 3 10 11 0 0 + 0 0.000000 0.00000E+00 + 14 4 3 10 11 0 0 + 0 0.000000 0.00000E+00 + 15 5 3 10 11 0 0 + 0 0.000000 0.00000E+00 + 16 3 5 8 9 0 0 + 0 0.000000 0.00000E+00 + 17 6 5 8 9 0 0 + 0 0.000000 0.00000E+00 + 18 7 5 8 9 0 0 + 0 0.000000 0.00000E+00 + 1 8 5 3 1 0.143000 diff --git a/src/data/amber_s/SER_C.frg b/src/data/amber_s/SER_C.frg new file mode 100644 index 0000000..a1041a8 --- /dev/null +++ b/src/data/amber_s/SER_C.frg @@ -0,0 +1,19 @@ +$SER_C + 12 1 1 0 +SER_C + 1 N N 1 1 0 1 1 -0.382100 0.000000 + 2 H H 0 0 0 1 1 0.268100 0.000000 + 3 CA CT 0 0 0 1 1 -0.272200 0.000000 + 4 HA H1 0 0 0 1 1 0.130400 0.000000 + 5 CB CT 0 0 0 1 1 0.112300 0.000000 + 62HB H1 0 0 0 1 1 0.081300 0.000000 + 73HB H1 0 0 0 1 1 0.081300 0.000000 + 8 OG OH 0 0 0 1 1 -0.651400 0.000000 + 9 HG HO 0 0 0 1 1 0.447400 0.000000 + 10 C C 0 1 0 1 1 0.811300 0.000000 + 11 O O2 0 0 0 1 1 -0.813200 0.000000 + 12 OXT O2 0 0 0 1 1 -0.813200 0.000000 + 2 1 3 10 11 + 4 3 5 8 9 + 6 5 7 + 10 12 diff --git a/src/data/amber_s/SER_C.sgm b/src/data/amber_s/SER_C.sgm new file mode 100644 index 0000000..f34b00f --- /dev/null +++ b/src/data/amber_s/SER_C.sgm @@ -0,0 +1,129 @@ +# +$SER_C + 4.600000 + 12 11 17 21 1 0 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.382100 0.000000 + 2 H 0 0 0 1 1 + H 0.268100 0.000000 + 3 CA 0 0 0 1 1 + CT -0.272200 0.000000 + 4 HA 0 0 0 1 1 + H1 0.130400 0.000000 + 5 CB 0 0 0 1 1 + CT 0.112300 0.000000 + 62HB 0 0 0 1 1 + H1 0.081300 0.000000 + 73HB 0 0 0 1 1 + H1 0.081300 0.000000 + 8 OG 0 0 0 1 1 + OH -0.651400 0.000000 + 9 HG 0 0 0 1 1 + HO 0.447400 0.000000 + 10 C 0 1 0 1 1 + C 0.811300 0.000000 + 11 O 0 0 0 1 1 + O2 -0.813200 0.000000 + 12 OXT 0 0 0 1 1 + O2 -0.813200 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 3 4 0 0 + 0.000000 0.00000E+00 + 4 3 5 0 0 + 0.000000 0.00000E+00 + 5 3 10 0 0 + 0.000000 0.00000E+00 + 6 5 6 0 0 + 0.000000 0.00000E+00 + 7 5 7 0 0 + 0.000000 0.00000E+00 + 8 5 8 0 0 + 0.000000 0.00000E+00 + 9 8 9 0 0 + 0.000000 0.00000E+00 + 10 10 11 0 0 + 0.000000 0.00000E+00 + 11 10 12 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 1 3 4 0 0 + 0.000000 0.00000E+00 + 3 1 3 5 0 0 + 0.000000 0.00000E+00 + 4 1 3 10 0 0 + 0.000000 0.00000E+00 + 5 4 3 5 0 0 + 0.000000 0.00000E+00 + 6 4 3 10 0 0 + 0.000000 0.00000E+00 + 7 5 3 10 0 0 + 0.000000 0.00000E+00 + 8 3 5 6 0 0 + 0.000000 0.00000E+00 + 9 3 5 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0.00000E+00 diff --git a/src/data/amber_s/SPC_M.sgm b/src/data/amber_s/SPC_M.sgm new file mode 100644 index 0000000..0f799af --- /dev/null +++ b/src/data/amber_s/SPC_M.sgm @@ -0,0 +1,17 @@ +# +$SPC_M + 4.600000 + 3 3 0 0 0 0 1 1 + 0.000000 + 1 OW 0 0 0 1 1 + OW -0.820000 0.000000 + 22HW 0 0 0 1 1 + HW 0.410000 0.000000 + 33HW 0 0 0 1 1 + HW 0.410000 0.000000 + 1 1 2 1 0 + 0.100000 0.50000E+06 + 2 1 3 1 0 + 0.100000 0.50000E+06 + 3 2 3 1 0 + 0.163330 0.50000E+06 diff --git a/src/data/amber_s/THR.frg b/src/data/amber_s/THR.frg new file mode 100644 index 0000000..0455f3b --- /dev/null +++ b/src/data/amber_s/THR.frg @@ -0,0 +1,21 @@ +$THR + 14 1 1 0 +THR + 1 N N 1 1 0 1 1 -0.415700 0.000000 + 2 H H 0 0 0 1 1 0.271900 0.000000 + 3 CA CT 0 0 0 1 1 -0.038900 0.000000 + 4 HA H1 0 0 0 1 1 0.100700 0.000000 + 5 CB CT 0 0 0 1 1 0.365400 0.000000 + 6 HB H1 0 0 0 1 1 0.004300 0.000000 + 7 CG2 CT 0 0 0 1 1 -0.243800 0.000000 + 82HG2 HC 0 0 0 1 1 0.064200 0.000000 + 93HG2 HC 0 0 0 1 1 0.064200 0.000000 + 104HG2 HC 0 0 0 1 1 0.064200 0.000000 + 11 OG1 OH 0 0 0 1 1 -0.676100 0.000000 + 12 HG1 HO 0 0 0 1 1 0.410200 0.000000 + 13 C C 2 1 0 1 1 0.597300 0.000000 + 14 O O 0 0 0 1 1 -0.567900 0.000000 + 2 1 3 13 14 + 4 3 5 11 12 + 6 5 7 8 + 9 7 10 diff --git a/src/data/amber_s/THR.sgm b/src/data/amber_s/THR.sgm new file mode 100644 index 0000000..12838f4 --- /dev/null +++ b/src/data/amber_s/THR.sgm @@ -0,0 +1,157 @@ +# +$THR + 4.600000 + 14 13 21 27 0 2 1 1 + 0.000000 + 1 N 1 1 0 1 1 + N -0.415700 0.000000 + 2 H 0 0 0 1 1 + H 0.271900 0.000000 + 3 CA 0 0 0 1 1 + CT -0.038900 0.000000 + 4 HA 0 0 0 1 1 + H1 0.100700 0.000000 + 5 CB 0 0 0 1 1 + CT 0.365400 0.000000 + 6 HB 0 0 0 1 1 + H1 0.004300 0.000000 + 7 CG2 0 0 0 1 1 + CT -0.243800 0.000000 + 82HG2 0 0 0 1 1 + HC 0.064200 0.000000 + 93HG2 0 0 0 1 1 + HC 0.064200 0.000000 + 104HG2 0 0 0 1 1 + HC 0.064200 0.000000 + 11 OG1 0 0 0 1 1 + OH -0.676100 0.000000 + 12 HG1 0 0 0 1 1 + HO 0.410200 0.000000 + 13 C 2 1 0 1 1 + C 0.597300 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a/src/data/amber_s/THR_N.frg b/src/data/amber_s/THR_N.frg new file mode 100644 index 0000000..3300834 --- /dev/null +++ b/src/data/amber_s/THR_N.frg @@ -0,0 +1,34 @@ +$THR_N + 16 1 1 0 +THR_N + 1 N N3 0 0 0 1 1 0.181200 0.000000 + 22H H 0 0 0 1 1 0.193400 0.000000 + 33H H 0 0 0 1 1 0.193400 0.000000 + 44H H 0 0 0 1 1 0.193400 0.000000 + 5 CA CT 0 0 0 1 1 0.003400 0.000000 + 6 HA HP 0 0 0 1 1 0.108700 0.000000 + 7 CB CT 0 0 0 1 1 0.451400 0.000000 + 8 HB H1 0 0 0 1 1 -0.032300 0.000000 + 9 CG2 CT 0 0 0 1 1 -0.255400 0.000000 + 102HG2 HC 0 0 0 1 1 0.062700 0.000000 + 113HG2 HC 0 0 0 1 1 0.062700 0.000000 + 124HG2 HC 0 0 0 1 1 0.062700 0.000000 + 13 OG1 OH 0 0 0 1 1 -0.676400 0.000000 + 14 HG1 HO 0 0 0 1 1 0.407000 0.000000 + 15 C C 2 1 0 1 1 0.616300 0.000000 + 16 O O 0 0 0 1 1 -0.572200 0.000000 + 2 1 + 3 1 + 4 1 + 5 1 + 6 5 + 7 5 + 8 7 + 9 7 + 10 9 + 11 9 + 12 9 + 13 7 + 14 13 + 15 5 + 16 15 diff --git a/src/data/amber_s/THR_N.sgm b/src/data/amber_s/THR_N.sgm new file mode 100644 index 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0.00000E+00 + 28 13 7 9 10 0 0 + 0 0.000000 0.00000E+00 + 29 13 7 9 11 0 0 + 0 0.000000 0.00000E+00 + 30 13 7 9 12 0 0 + 0 0.000000 0.00000E+00 + 31 8 7 13 14 0 0 + 0 0.000000 0.00000E+00 + 32 8 7 13 15 0 0 + 0 0.000000 0.00000E+00 + 33 8 7 13 16 0 0 + 0 0.000000 0.00000E+00 + 34 5 7 13 14 0 0 + 0 0.000000 0.00000E+00 + 35 5 7 13 15 0 0 + 0 0.000000 0.00000E+00 + 36 5 7 13 16 0 0 + 0 0.000000 0.00000E+00 + 37 9 7 13 14 0 0 + 0 0.000000 0.00000E+00 + 38 9 7 13 15 0 0 + 0 0.000000 0.00000E+00 + 39 9 7 13 16 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_s/ZN.frg b/src/data/amber_s/ZN.frg new file mode 100644 index 0000000..15c07a1 --- /dev/null +++ b/src/data/amber_s/ZN.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$ZN + 1 1 1 0 +ZN + 1ZN ZN 3 0 0 1 1 2.000000 0.000000 diff --git a/src/data/amber_s/amber.par b/src/data/amber_s/amber.par new file mode 100644 index 0000000..1eef736 --- /dev/null +++ b/src/data/amber_s/amber.par @@ -0,0 +1,1101 @@ +# +#This is the AMBER99 standard parameter file for NWChem 4.0 +# +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +# +Atoms +C 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CA 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CB 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CC 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CD 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CK 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CM 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CN 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CQ 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CR 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CT 12.01000 4.57730E-01 1.90800E-01 1 1111111111 + 6 2.28865E-01 1.90800E-01 +CV 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CW 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +C* 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CY 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CZ 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +C0 40.08000 1.92376E+00 1.71310E-01 1 1111111111 + 6 9.61880E-01 1.71310E-01 +H 1.00800 6.56888E-02 6.00000E-02 1 1111111111 + 1 3.28444E-02 6.00000E-02 +HC 1.00800 6.56888E-02 1.48700E-01 1 1111111111 + 1 3.28444E-02 1.48700E-01 +H1 1.00800 6.56888E-02 1.38700E-01 1 1111111111 + 1 3.28444E-02 1.38700E-01 +H2 1.00800 6.56888E-02 1.28700E-01 1 1111111111 + 1 3.28444E-02 1.28700E-01 +H3 1.00800 6.56888E-02 1.18700E-01 1 1111111111 + 1 3.28444E-02 1.18700E-01 +HA 1.00800 6.27600E-02 1.45900E-01 1 1111111111 + 1 3.13800E-02 1.45900E-01 +H4 1.00800 6.27600E-02 1.40900E-01 1 1111111111 + 1 3.13800E-02 1.40900E-01 +H5 1.00800 6.27600E-02 1.35900E-01 1 1111111111 + 1 3.13800E-02 1.35900E-01 +HO 1.00800 0.00000E+00 0.00000E+00 1 1111111111 + 1 0.00000E+00 0.00000E+00 +HS 1.00800 6.56888E-02 6.00000E-02 1 1111111111 + 1 3.28444E-02 6.00000E-02 +HW 1.00800 0.00000E+00 0.00000E+00 1 1111111111 + 1 0.00000E+00 0.00000E+00 +HP 1.00800 6.56888E-02 1.10000E-01 1 1111111111 + 1 3.28444E-02 1.10000E-01 +HZ 1.00800 6.27600E-02 1.45900E-01 1 1111111111 + 1 3.13800E-02 1.45900E-01 +F 19.00000 2.55224E-01 1.75000E-01 1 1111111111 + 9 1.27612E-01 1.75000E-01 +CL 35.45000 1.10876E+00 1.94800E-01 1 1111111111 + 17 5.54380E-01 1.94800E-01 +BR 79.90000 1.33888E+00 2.22000E-01 1 1111111111 + 35 6.69440E-01 2.22000E-01 +I 126.90000 1.67360E+00 2.35000E-01 1 1111111111 + 53 8.36800E-01 2.35000E-01 +IM 35.45000 4.18400E-01 2.47000E-01 1 1111111111 + 17 2.09200E-01 2.47000E-01 +IB 131.00000 4.18400E-01 5.00000E-01 1 1111111111 + 54 2.09200E-01 5.00000E-01 +MG 24.30500 3.74342E+00 7.92600E-02 1 1111111111 + 12 1.87171E+00 7.92600E-02 +N 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NA 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NB 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NC 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +N2 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +N3 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NT 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +N* 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NY 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +O 16.00000 8.78640E-01 1.66120E-01 1 1111111111 + 8 4.39320E-01 1.66120E-01 +O2 16.00000 8.78640E-01 1.66120E-01 1 1111111111 + 8 4.39320E-01 1.66120E-01 +OW 16.00000 6.35968E-01 1.76830E-01 1 1111111111 + 8 3.17984E-01 1.76830E-01 +OH 16.00000 8.80314E-01 1.72100E-01 1 1111111111 + 8 4.40157E-01 1.72100E-01 +OS 16.00000 7.11280E-01 1.68370E-01 1 1111111111 + 8 3.55640E-01 1.68370E-01 +P 30.97000 8.36800E-01 2.10000E-01 1 1111111111 + 15 4.18400E-01 2.10000E-01 +S 32.06000 1.04600E+00 2.00000E-01 1 1111111111 + 16 5.23000E-01 2.00000E-01 +SH 32.06000 1.04600E+00 2.00000E-01 1 1111111111 + 16 5.23000E-01 2.00000E-01 +CU 63.55000 0.00000E+00 0.00000E+00 1 1111111111 + 29 0.00000E+00 0.00000E+00 +FE 55.00000 0.00000E+00 0.00000E+00 1 1111111111 + 26 0.00000E+00 0.00000E+00 +Li 6.94000 7.65672E-02 1.13700E-01 1 1111111111 + 3 3.82836E-02 1.13700E-01 +IP 22.99000 1.15897E-02 1.86800E-01 1 1111111111 + 11 5.79485E-03 1.86800E-01 +Na 22.99000 1.15897E-02 1.86800E-01 1 1111111111 + 11 5.79485E-03 1.86800E-01 +K 39.10000 1.37235E-03 2.65800E-01 1 1111111111 + 19 6.86175E-04 2.65800E-01 +Rb 85.47000 7.11280E-04 2.95600E-01 1 1111111111 + 37 3.55640E-04 2.95600E-01 +Cs 132.91000 3.37230E-04 3.39500E-01 1 1111111111 + 55 1.68615E-04 3.39500E-01 +Zn 65.40000 5.23000E-02 1.10000E-01 1 1111111111 + 30 2.61500E-02 1.10000E-01 +LP 3.00000 0.00000E+00 0.00000E+00 1 1111111111 + 0 0.00000E+00 0.00000E+00 +Cross +Bonds +HW -OW 0.09570 4.62750E+05 +HW -HW 0.15130 4.62750E+05 +C -C 0.15250 2.59408E+05 +C -CA 0.14090 3.92459E+05 +C -CB 0.14190 3.74050E+05 +C -CM 0.14440 3.43088E+05 +C -CT 0.15220 2.65266E+05 +C -N 0.13350 4.10032E+05 0.070000 +C -N* 0.13830 3.54803E+05 0.070000 +C -NA 0.13880 3.49782E+05 0.070000 +C -NC 0.13580 3.82418E+05 0.070000 +C -O 0.12290 4.76976E+05 0.570000 +C -O2 0.12500 5.48941E+05 0.570000 +C -OH 0.13640 3.76560E+05 0.300000 +C -OS 0.13230 3.76560E+05 +C -H4 0.10800 3.07106E+05 +C -H5 0.10800 3.07106E+05 +CA -CA 0.14000 3.92459E+05 +CA -CB 0.14040 3.92459E+05 +CA -CM 0.14330 3.57314E+05 +CA -CN 0.14000 3.92459E+05 +CA -CT 0.15100 2.65266E+05 +CA -HA 0.10800 3.07106E+05 -0.050000 +CA -H4 0.10800 3.07106E+05 -0.050000 +CA -N2 0.13400 4.02501E+05 0.070000 +CA -NA 0.13810 3.57314E+05 0.070000 +CA -NC 0.13390 4.04174E+05 0.070000 +CA -OH 0.13640 3.76560E+05 +CB -CB 0.13700 4.35136E+05 +CB -N* 0.13740 3.64845E+05 0.070000 +CB -NB 0.13910 3.46435E+05 0.070000 +CB -NC 0.13540 3.85765E+05 0.070000 +CD -HA 0.10800 3.07106E+05 +CD -CD 0.14000 3.92459E+05 +CD -CM 0.13500 4.59403E+05 +CD -CT 0.15100 2.65266E+05 +CK -H5 0.10800 3.07106E+05 -0.050000 +CK -N* 0.13710 3.68192E+05 0.070000 +CK -NB 0.13040 4.42667E+05 0.070000 +CM -CM 0.13500 4.59403E+05 +CM -CT 0.15100 2.65266E+05 +CM -HA 0.10800 3.07106E+05 -0.050000 +CM -H4 0.10800 3.07106E+05 -0.050000 +CM -H5 0.10800 3.07106E+05 -0.050000 +CM -N* 0.13650 3.74886E+05 0.070000 +CM -OS 0.12400 4.01664E+05 +CQ -H5 0.10800 3.07106E+05 -0.050000 +CQ -NC 0.13240 4.20074E+05 0.070000 +CT -CT 0.15260 2.59408E+05 +CT -HC 0.10900 2.84512E+05 -0.050000 +CT -H1 0.10900 2.84512E+05 -0.050000 +CT -H2 0.10900 2.84512E+05 -0.050000 +CT -H3 0.10900 2.84512E+05 -0.050000 +CT -HP 0.10900 2.84512E+05 -0.050000 +CT -N* 0.14750 2.82002E+05 0.070000 +CT -N2 0.14630 2.82002E+05 0.070000 +CT -OH 0.14100 2.67776E+05 0.300000 +CT -OS 0.14100 2.67776E+05 0.300000 +C* -HC 0.10800 3.07106E+05 -0.050000 +C* -CB 0.14590 3.24678E+05 +C* -CT 0.14950 2.65266E+05 +C* -CW 0.13520 4.56893E+05 +CB -CN 0.14190 3.74050E+05 +CC -CT 0.15040 2.65266E+05 +CC -CV 0.13750 4.28442E+05 +CC -CW 0.13710 4.33462E+05 +CC -NA 0.13850 3.53130E+05 0.070000 +CC -NB 0.13940 3.43088E+05 0.070000 +CN -NA 0.13800 3.58150E+05 0.070000 +CR -H5 0.10800 3.07106E+05 -0.050000 +CR -NA 0.13430 3.99154E+05 0.070000 +CR -NB 0.13350 4.08358E+05 0.070000 +CT -N 0.14490 2.82002E+05 0.070000 +CT -N3 0.14710 3.07106E+05 0.070000 +CT -NT 0.14710 3.07106E+05 +CT -S 0.18100 1.89954E+05 0.110000 +CT -SH 0.18100 1.98322E+05 0.110000 +CT -CY 0.14580 3.34720E+05 +CT -CZ 0.14590 3.34720E+05 +CV -H4 0.10800 3.07106E+05 -0.050000 +CV -NB 0.13940 3.43088E+05 0.070000 +CW -H4 0.10800 3.07106E+05 -0.050000 +CW -NA 0.13810 3.57314E+05 0.070000 +CY -NY 0.11500 5.02080E+05 +CZ -CZ 0.12060 5.02080E+05 +CZ -HZ 0.10560 3.34720E+05 +O2 -P 0.14800 4.39320E+05 +OH -P 0.16100 1.92464E+05 +OS -P 0.16100 1.92464E+05 +H -N2 0.10100 3.63171E+05 0.270000 +H -N* 0.10100 3.63171E+05 0.270000 +H -NA 0.10100 3.63171E+05 0.270000 +H -N 0.10100 3.63171E+05 0.270000 +H -N3 0.10100 3.63171E+05 0.270000 +H -NT 0.10100 3.63171E+05 +HO -OH 0.09600 4.62750E+05 0.190000 +HO -OS 0.09600 4.62750E+05 0.190000 +HS -SH 0.13360 2.29283E+05 0.190000 +S -S 0.20380 1.38909E+05 +CT -F 0.13800 3.07106E+05 +CT -CL 0.17660 1.94138E+05 +BR -CT 0.19440 1.33051E+05 +CT -I 0.21660 1.23846E+05 +CA -F 0.13590 3.23005E+05 +CA -CL 0.17270 1.61502E+05 +CA -I 0.20750 1.43093E+05 +BR -CA 0.18900 1.43930E+05 +LP -O 0.02000 5.02080E+05 +LP -OH 0.02000 5.02080E+05 +LP -OS 0.02000 5.02080E+05 +LP -N3 0.02000 5.02080E+05 +LP -NT 0.02000 5.02080E+05 +LP -NB 0.02000 5.02080E+05 +LP -NC 0.02000 5.02080E+05 +LP -S 0.07000 5.02080E+05 +LP -SH 0.07000 5.02080E+05 +Angles +HW -OW -HW 1.82422 8.36800E+02 +HW -HW -OW 2.22948 0.00000E+00 +C -C -O 2.09440 6.69440E+02 +C -C -OH 2.09440 6.69440E+02 +CA -C -CA 2.09440 5.27184E+02 +CA -C -OH 2.09440 5.85760E+02 +CB -C -NA 1.94255 5.85760E+02 +CB -C -O 2.24798 6.69440E+02 +CM -C -NA 1.99142 5.85760E+02 +CM -C -O 2.18690 6.69440E+02 +CT -C -O 2.10138 6.69440E+02 +CT -C -O2 2.04204 5.85760E+02 +CT -C -N 2.03505 5.85760E+02 +CT -C -CT 2.04204 5.27184E+02 +CT -C -OS 2.00713 6.69440E+02 +CT -C -OH 1.91986 6.69440E+02 +N* -C -NA 2.01411 5.85760E+02 +N* -C -NC 2.06996 5.85760E+02 +N* -C -O 2.11010 6.69440E+02 +NA -C -O 2.10487 6.69440E+02 +NC -C -O 2.13803 6.69440E+02 +N -C -O 2.14501 6.69440E+02 +O -C -O 2.19911 6.69440E+02 +O -C -OH 2.09440 6.69440E+02 +O -C -OS 2.18166 6.69440E+02 +O2 -C -O2 2.19911 6.69440E+02 +C -C -H4 2.09440 4.18400E+02 +CM -C -H4 2.00713 4.18400E+02 +CT -C -H4 2.00713 4.18400E+02 +H4 -C -O 2.09440 4.18400E+02 +H4 -C -OH 2.09440 4.18400E+02 +H5 -C -N 2.09440 4.18400E+02 +H5 -C -O 2.07694 4.18400E+02 +H5 -C -OH 1.86750 4.18400E+02 +H5 -C -OS 1.86750 4.18400E+02 +C -CA -CA 2.09440 5.27184E+02 +C -CA -HA 2.09440 4.18400E+02 +CA -CA -CA 2.09440 5.27184E+02 +CA -CA -CB 2.09440 5.27184E+02 +CA -CA -CT 2.09440 5.85760E+02 +CA -CA -HA 2.09440 4.18400E+02 +CA -CA -H4 2.09440 4.18400E+02 +CA -CA -OH 2.09440 5.85760E+02 +CA -CA -CN 2.09440 5.27184E+02 +CB -CA -HA 2.09440 4.18400E+02 +CB -CA -H4 2.09440 4.18400E+02 +CB -CA -N2 2.15548 5.85760E+02 +CB -CA -NC 2.04727 5.85760E+02 +CM -CA -N2 2.09614 5.85760E+02 +CM -CA -NC 2.12057 5.85760E+02 +CN -CA -HA 2.09440 4.18400E+02 +NA -CA -NC 2.15199 5.85760E+02 +N2 -CA -NA 2.02458 5.85760E+02 +N2 -CA -NC 2.08218 5.85760E+02 +N2 -CA -N2 2.09440 5.85760E+02 +CA -CA -F 2.11185 5.85760E+02 +CA -CA -CL 2.07345 5.85760E+02 +BR -CA -CA 2.07345 5.85760E+02 +CA -CA -I 2.07345 5.85760E+02 +C -CB -CB 2.08043 5.27184E+02 +C -CB -NB 2.26893 5.85760E+02 +CA -CB -CB 2.04727 5.27184E+02 +CA -CB -NB 2.31082 5.85760E+02 +CB -CB -N* 1.85354 5.85760E+02 +CB -CB -NB 1.92684 5.85760E+02 +CB -CB -NC 2.22879 5.85760E+02 +C* -CB -CA 2.35445 5.27184E+02 +C* -CB -CN 1.89892 5.27184E+02 +CA -CB -CN 2.02807 5.27184E+02 +N* -CB -NC 2.20261 5.85760E+02 +CD -CD -CM 2.09440 5.27184E+02 +CD -CD -CT 2.09440 5.85760E+02 +CM -CD -CT 2.09440 5.85760E+02 +HA -CD -HA 2.07694 2.92880E+02 +CD -CD -HA 2.09440 4.18400E+02 +CM -CD -HA 2.09440 4.18400E+02 +H5 -CK -N* 2.14763 4.18400E+02 +H5 -CK -NB 2.14763 4.18400E+02 +N* -CK -NB 1.98793 5.85760E+02 +C -CM -CM 2.10661 5.27184E+02 +C -CM -CT 2.08916 5.85760E+02 +C -CM -HA 2.08916 4.18400E+02 +C -CM -H4 2.08916 4.18400E+02 +CA -CM -CM 2.04204 5.27184E+02 +CA -CM -HA 2.15199 4.18400E+02 +CA -CM -H4 2.15199 4.18400E+02 +CM -CM -CT 2.08916 5.85760E+02 +CM -CM -HA 2.08916 4.18400E+02 +CM -CM -H4 2.08916 4.18400E+02 +CM -CM -N* 2.11534 5.85760E+02 +CM -CM -OS 2.18166 6.69440E+02 +H4 -CM -N* 2.07869 4.18400E+02 +H4 -CM -OS 1.97222 4.18400E+02 +HA -CM -HA 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1.82212 5.85760E+02 +CT -CY -NY 3.14159 6.69440E+02 +CT -CZ -CZ 3.14159 6.69440E+02 +CZ -CZ -HZ 3.14159 4.18400E+02 +C -N -CT 2.12756 4.18400E+02 +C -N -H 2.09440 4.18400E+02 +CT -N -H 2.06019 4.18400E+02 +CT -N -CT 2.05949 4.18400E+02 +H -N -H 2.09440 2.92880E+02 +C -N* -CM 2.12232 5.85760E+02 +C -N* -CT 2.05251 5.85760E+02 +C -N* -H 2.08043 4.18400E+02 +CB -N* -CK 1.83958 5.85760E+02 +CB -N* -CT 2.19562 5.85760E+02 +CB -N* -H 2.19562 4.18400E+02 +CK -N* -CT 2.24798 5.85760E+02 +CK -N* -H 2.24798 4.18400E+02 +CM -N* -CT 2.11534 5.85760E+02 +CM -N* -H 2.11534 4.18400E+02 +CA -N2 -H 2.09440 4.18400E+02 +CA -N2 -CT 2.15025 4.18400E+02 +CT -N2 -H 2.06647 4.18400E+02 +H -N2 -H 2.09440 2.92880E+02 +CT -N3 -H 1.91114 4.18400E+02 +CT -N3 -CT 1.91114 4.18400E+02 +H -N3 -H 1.91114 2.92880E+02 +CT -NT -H 1.91114 4.18400E+02 +CT -NT -CT 1.91114 4.18400E+02 +H -NT -H 1.91114 2.92880E+02 +C -NA -C 2.20610 5.85760E+02 +C -NA -CA 2.18515 5.85760E+02 +C -NA -H 2.03854 4.18400E+02 +CA -NA -H 2.05949 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1.60692 2.92880E+02 +CB -NB -LP 2.19911 1.25520E+03 +CC -NB -LP 2.19911 1.25520E+03 +CK -NB -LP 2.19911 1.25520E+03 +CR -NB -LP 2.19911 1.25520E+03 +CV -NB -LP 2.19911 1.25520E+03 +C -NC -LP 2.09440 1.25520E+03 +CA -NC -LP 2.09440 1.25520E+03 +CB -NC -LP 2.09440 1.25520E+03 +CQ -NC -LP 2.09440 1.25520E+03 +CT -N3 -LP 1.91114 1.25520E+03 +H -N3 -LP 1.91114 1.25520E+03 +CT -NT -LP 1.91114 1.25520E+03 +H -NT -LP 1.91114 1.25520E+03 +C -O -LP 2.09440 1.25520E+03 +LP -O -LP 2.09440 1.25520E+03 +C -OH -LP 2.09440 1.25520E+03 +CT -OH -LP 1.91114 1.25520E+03 +HO -OH -LP 1.91114 1.25520E+03 +LP -OH -LP 1.91114 1.25520E+03 +C -OS -LP 1.91114 1.25520E+03 +CM -OS -LP 1.91114 1.25520E+03 +CT -OS -LP 1.91114 1.25520E+03 +LP -OS -LP 1.91114 1.25520E+03 +CT -S -LP 1.57080 1.25520E+03 +CT -SH -LP 1.57080 1.25520E+03 +LP -OS -P 1.91114 1.25520E+03 +LP -S -LP 3.14159 1.25520E+03 +LP -SH -LP 3.14159 1.25520E+03 +HS -SH -LP 1.57080 1.25520E+03 +Proper dihedrals + -C -C - 3.14159 1.51670E+01 2 + -C -CA - 3.14159 1.51670E+01 2 + -C -CB - 3.14159 1.25520E+01 2 + -C -CM - 3.14159 9.10020E+00 2 + -C -CT - 0.00000 0.00000E+00 2 + -C -N - 3.14159 1.04600E+01 2 + -C -N* - 3.14159 6.06680E+00 2 + -C -NA - 3.14159 5.64840E+00 2 + -C -NC - 3.14159 1.67360E+01 2 + -C -O - 3.14159 1.17152E+01 2 + -C -OH - 3.14159 9.62320E+00 2 + -C -OS - 3.14159 1.12968E+01 2 + -CA -CA - 3.14159 1.51670E+01 2 + -CA -CB - 3.14159 1.46440E+01 2 + -CA -CM - 3.14159 1.06692E+01 2 + -CA -CN - 3.14159 1.51670E+01 2 + -CA -CT - 0.00000 0.00000E+00 2 + -CA -N2 - 3.14159 1.00416E+01 2 + -CA -NA - 3.14159 6.27600E+00 2 + -CA -NC - 3.14159 2.00832E+01 2 + -CA -OH - 3.14159 3.76560E+00 2 + -CB -CB - 3.14159 2.28028E+01 2 + -CB -CN - 3.14159 1.25520E+01 2 + -CB -N* - 3.14159 6.90360E+00 2 + -CB -NB - 3.14159 1.06692E+01 2 + -CB -NC - 3.14159 1.73636E+01 2 + -CC -CT - 0.00000 0.00000E+00 2 + -CC -CV - 3.14159 2.15476E+01 2 + -CC -CW - 3.14159 2.24890E+01 2 + -CC -NA - 3.14159 5.85760E+00 2 + -CC -NB - 3.14159 1.00416E+01 2 + 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3.14159 6.27600E+00 2 + -OH -P - 0.00000 1.04600E+00 3 + -OS -P - 0.00000 1.04600E+00 3 +N -C -CT -N 3.14159 7.11280E+00 -1 +N -C -CT -N 3.14159 8.36800E+00 2 +C -CT -N -C 3.14159 3.55640E+00 -2 +C -CT -N -C 0.00000 3.34720E+00 1 +CT -CT -N -C 3.14159 2.09200E+00 -4 +CT -CT -N -C 3.14159 6.27600E-01 -3 +CT -CT -N -C 0.00000 2.21752E+00 1 +N -C -CT -CT 0.00000 4.18400E-01 -4 +N -C -CT -CT 0.00000 2.92880E-01 2 +O -C -N -H 3.14159 1.04600E+01 -2 +O -C -N -H 0.00000 8.36800E+00 1 +CT -S -S -CT 0.00000 1.46440E+01 -2 +CT -S -S -CT 0.00000 2.51040E+00 3 +CT -OS -P -OH 0.00000 1.04600E+00 -3 +CT -OS -P -OH 0.00000 5.02080E+00 2 +CT -OS -P -OS 0.00000 1.04600E+00 -3 +CT -OS -P -OS 0.00000 5.02080E+00 2 +O -C -CT -H1 0.00000 3.34720E+00 -1 +O -C -CT -H1 3.14159 3.34720E-01 3 +O -C -CT -HC 0.00000 3.34720E+00 -1 +O -C -CT -HC 3.14159 3.34720E-01 3 +HC -CT -CT -HC 0.00000 6.27600E-01 3 +HC -CT -CT -CT 0.00000 6.69440E-01 3 +CM -CM -CT -HC 3.14159 1.58992E+00 -3 +CM -CM -CT -HC 0.00000 4.81160E+00 1 +CT -CT -OH -HO 0.00000 6.69440E-01 -3 +CT -CT -OH -HO 0.00000 1.04600E+00 1 +O -C -OH -HO 3.14159 9.62320E+00 -2 +O -C -OH -HO 0.00000 7.94960E+00 1 +O -C -CM -CM 3.14159 9.10020E+00 -2 +O -C -CM -CM 0.00000 1.25520E+00 3 +CT -CM -CM -CT 3.14159 2.78236E+01 -2 +CT -CM -CM -CT 3.14159 7.94960E+00 1 +CT -CT -CT -CT 0.00000 7.53120E-01 -3 +CT -CT -CT -CT 3.14159 1.04600E+00 -2 +CT -CT -CT -CT 3.14159 8.36800E-01 1 +CT -CT -NT -CT 0.00000 1.25520E+00 -3 +CT -CT -NT -CT 3.14159 2.00832E+00 2 +CT -CT -OS -CT 0.00000 1.60247E+00 -3 +CT -CT -OS -CT 3.14159 4.18400E-01 2 +CT -CT -OS -C 0.00000 1.60247E+00 -3 +CT -CT -OS -C 3.14159 3.34720E+00 1 +OS -CT -OS -CT 0.00000 4.18400E-01 -3 +OS -CT -OS -CT 3.14159 3.55640E+00 -2 +OS -CT -OS -CT 3.14159 5.64840E+00 1 +N* -CT -OS -CT 0.00000 1.60247E+00 -3 +N* -CT -OS -CT 0.00000 2.71960E+00 2 +CT -CZ -CZ -HZ 0.00000 0.00000E+00 1 +O -C -OS -CT 3.14159 1.12968E+01 -2 +O -C -OS -CT 3.14159 5.85760E+00 1 +OS -CT -N* -CK 0.00000 0.00000E+00 -2 +OS -CT -N* -CK 0.00000 1.04600E+01 1 +OS -CT -N* -CM 0.00000 0.00000E+00 -2 +OS -CT -N* -CM 0.00000 1.04600E+01 1 +OS -CT -CT -OS 0.00000 6.02496E-01 -3 +OS -CT -CT -OS 0.00000 4.91620E+00 2 +OS -CT -CT -OH 0.00000 6.02496E-01 -3 +OS -CT -CT -OH 0.00000 4.91620E+00 2 +OH -CT -CT -OH 0.00000 6.02496E-01 -3 +OH -CT -CT -OH 0.00000 4.91620E+00 2 +F -CT -CT -F 3.14159 5.02080E+00 1 +CL -CT -CT -CL 3.14159 1.88280E+00 1 +BR -CT -CT -BR 3.14159 0.00000E+00 1 +H1 -CT -CT -OS 0.00000 1.04600E+00 1 +H1 -CT -CT -OH 0.00000 1.04600E+00 1 +H1 -CT -CT -F 0.00000 7.94960E-01 1 +H1 -CT -CT -CL 0.00000 1.04600E+00 1 +H1 -CT -CT -BR 0.00000 2.30120E+00 1 +HC -CT -CT -OS 0.00000 1.04600E+00 1 +HC -CT -CT -OH 0.00000 1.04600E+00 1 +HC -CT -CT -f 0.00000 7.94960E-01 1 +HC -CT -CT -CL 0.00000 1.04600E+00 1 +HC -CT -CT -BR 0.00000 2.30120E+00 1 +H1 -CT -NT -LP 0.00000 0.00000E+00 3 +CT -CT -NT -LP 0.00000 0.00000E+00 3 +CT -C -N -LP 3.14159 0.00000E+00 2 +O -C -N -LP 3.14159 0.00000E+00 2 +H1 -CT -OH -LP 0.00000 0.00000E+00 3 +CT -CT -OH -LP 0.00000 0.00000E+00 3 +H1 -CT -OS -LP 0.00000 0.00000E+00 3 +H2 -CT -OS -LP 0.00000 0.00000E+00 3 +CT -CT -OS -LP 0.00000 0.00000E+00 3 +CM -CM -OS -LP 3.14159 0.00000E+00 2 +HA -CM -OS -LP 3.14159 0.00000E+00 2 +H4 -CM -OS -LP 3.14159 0.00000E+00 2 +Improper dihedrals + - -C -O 3.14159 4.39320E+01 2 + -O2 -C -O2 3.14159 4.39320E+01 2 + - -N -H 3.14159 4.18400E+00 2 + - -N2 -H 3.14159 4.18400E+00 2 + - -NA -H 3.14159 4.18400E+00 2 + -N2 -CA -N2 3.14159 4.39320E+01 2 + -CT -N -CT 3.14159 4.18400E+00 2 + - -CA -HA 3.14159 4.60240E+00 2 + - -CW -H4 3.14159 4.60240E+00 2 + - -CR -H5 3.14159 4.60240E+00 2 + - -CV -H4 3.14159 4.60240E+00 2 + - -CQ -H5 3.14159 4.60240E+00 2 + - -CK -H5 3.14159 4.60240E+00 2 + - -CM -H4 3.14159 4.60240E+00 2 + - -CM -HA 3.14159 4.60240E+00 2 + - -CA -H4 3.14159 4.60240E+00 2 + - -CA -H5 3.14159 4.60240E+00 2 +CK -CB -N* -CT 3.14159 4.18400E+00 2 +CM -C -N* -CT 3.14159 4.18400E+00 2 +CM -C -CM -CT 3.14159 4.60240E+00 2 +CT -O -C -OH 3.14159 4.39320E+01 2 +NA -CV -CC -CT 3.14159 4.60240E+00 2 +NB -CW -CC -CT 3.14159 4.60240E+00 2 +NA -CW -CC -CT 3.14159 4.60240E+00 2 +CW -CB -C* -CT 3.14159 4.60240E+00 2 +CA -CA -CA -CT 3.14159 4.60240E+00 2 +C -CM -CM -CT 3.14159 4.60240E+00 2 +NC -CM -CA -N2 3.14159 4.60240E+00 2 +CB -NC -CA -N2 3.14159 4.60240E+00 2 +NA -NC -CA -N2 3.14159 4.60240E+00 2 +CA -CA -C -OH 3.14159 4.60240E+00 2 +CA -CA -CA -OH 3.14159 4.60240E+00 2 +H5 -O -C -OH 3.14159 4.60240E+00 2 +H5 -O -C -OS 3.14159 4.60240E+00 2 +CM -CT -CM -HA 3.14159 4.60240E+00 2 +CA -CA -CA -BR 3.14159 4.60240E+00 2 +CM -H4 -C -O 3.14159 4.60240E+00 2 +C -CT -N -H 3.14159 4.60240E+00 2 +C -CT -N -O 3.14159 4.60240E+00 2 +# +Atom types +# +# Definition of the atom types +# +# This file contains the definition of AMBER atom types in terms of number and +# type of neighbor atoms. +# +# Note that the order in which the definitions are given is important. +# For each atom the last applicable entry in this file will be used, i.e. +# atom type definitions are given in increasing specificity. +# +# Atomic number increased by 200 means singly protonated +# 400 doubly +# 600 triply +# 800 un-protonated +# 1000 one non-hydrogen +# 2000 two non-hydrogens +# 3000 three non-hydrogens +# 4000 four non-hydrogens +# +# Atom number 3500 would signify any unprotonated atom with three non-hydrogens +# +# +# Each entry contains: +# +# 1 a4 atom type name +# +# 2 i7 atomic number +# +# 3 i3 atom saturation : 0 = undetermined, always applies +# 1 = aliphatic; +# 2 = double bond; +# 3 = aromatic; +# +# 4 i5 aliphatic ring : -1 = not in aliphatic ring +# 0 = any +# 1 = in at least one aliphatic ring +# 3 = in 3-membered aliphatic ring +# 4 = in 4-membered aliphatic ring +# 5 = in 5-membered aliphatic ring +# 6 = in 6-membered aliphatic ring +# 56 = junction 5 & 6 membered aliphatic rings +# 66 = junction two 6 membered aliphatic rings +# +# 5 i5 aromatic ring : -1 = not in aromatic ring +# 0 = any +# 1 = in at least one aromatic ring +# 5 = in 5-membered aromatic ring +# 6 = in 6-membered aromatic ring +# 56 = junction 5 & 6 membered aromatic rings +# 66 = junction two 6 membered aromatic rings +# 666 = junction three 6 membered aromatic rings +# +# 6 i3 number of neighbors : -1 = no neighbors +# 0 = any number of neighbors +# +# 7 i7 atom num neighbor 1 +# +# 8 i3 num n1 neighbors 0 = any number of neighbors +# +# 9 i7 atom num neighb n11 +# +# 10 i7 atom num neighb n12 +# +# 11 i7 atom num neighb n13 +# +# 12 i7 atom num neighbor 2 +# +# 13 i3 num n2 neighbors 0 = any number of neighbors +# +# 14 i7 atom num neighb n21 +# +# 15 i7 atom num neighb n22 +# +# 16 i7 atom num neighb n23 +# +# 17 i7 atom num neighbor 3 +# +# 18 i3 num n3 neighbors 0 = any number of neighbors +# +# 19 i7 atom num neighb n31 +# +# 20 i7 atom num neighb n32 +# +# 21 i7 atom num neighb n33 +# +# +# +# 1 2 3 4 5 +#23456789 123456789 123456789 123456789 123456789 12345678 +# 1 2 3 4 5 6 7 8 9 10 11 +# 12 13 14 15 16 +# 17 18 19 20 21 +# +H 1 0 0 0 1 7 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HO 1 0 0 0 1 208 2 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HS 1 0 0 0 1 16 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HA 1 0 0 0 1 6 3 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HC 1 0 0 0 1 6 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H1 1 0 0 0 1 6 4 7 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H1 1 0 0 0 1 6 4 8 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H1 1 0 0 0 1 6 4 16 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H2 1 0 0 0 1 6 4 7 7 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H2 1 0 0 0 1 6 4 7 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H2 1 0 0 0 1 6 4 8 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 7 7 7 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 7 7 8 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 7 8 8 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 8 8 8 + 0 0 0 0 0 + 0 0 0 0 0 +# +HP 1 0 0 0 1 6 4 607 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HP 1 0 0 0 1 6 4 1407 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H4 1 0 0 0 1 6 3 7 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H4 1 0 0 0 1 6 3 8 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H5 1 0 0 0 1 6 3 7 7 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H5 1 0 0 0 1 6 3 7 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H5 1 0 0 0 1 6 3 8 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HW 1 0 0 0 1 408 2 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CT 6 0 0 0 4 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CA 6 2 0 0 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# CZ in arginine +# +CA 6 0 0 0 3 207 3 0 0 0 + 407 3 0 0 0 + 407 3 0 0 0 +# +# aromatic carbon in 6-membered ring +# +CA 6 0 0 6 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CM 6 2 0 0 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +C 6 0 0 0 3 8 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CV 6 0 0 5 3 6 0 0 0 0 + 7 2 0 0 0 + 0 0 0 0 0 +# +CB 6 0 0 56 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CR 6 0 0 5 3 7 0 0 0 0 + 7 0 0 0 0 + 0 0 0 0 0 +# +CK 6 0 0 5 3 807 3 0 0 0 + 7 0 0 0 0 + 0 0 0 0 0 +# +CW 6 0 0 5 3 6 0 0 0 0 + 207 0 0 0 0 + 0 0 0 0 0 +# +C* 6 0 0 5 3 6 0 0 0 0 + 6 0 0 0 0 + 0 0 0 0 0 +# +CC 806 0 0 5 3 7 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CN 6 0 0 56 3 206 0 0 0 0 + 207 0 0 0 0 + 0 0 0 0 0 +# +CQ 6 0 0 6 3 7 2 0 0 0 + 7 2 0 0 0 + 0 0 0 0 0 +# +# guanidinium ion +# +N2 7 0 0 0 3 6 3 7 7 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# aromatic amine +# +N2 7 0 0 0 3 6 3 0 0 0 + 1 1 0 0 0 + 1 1 0 0 0 +# +N2 7 0 0 0 3 6 3 0 0 0 + 6 3 0 0 0 + 0 0 0 0 0 +# +N 7 0 0 0 3 6 3 8 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +# proline +# +N 7 0 0 0 3 6 3 8 6 0 + 6 4 6 6 1 + 6 4 6 1 1 +# +NA 207 0 0 5 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +NA 207 0 0 6 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +NB 7 0 0 5 2 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +NC 7 0 0 6 2 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N* 7 0 0 5 3 6 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N* 7 0 0 6 3 6 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N3 7 0 0 0 4 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# NE in arginine +# +N2 7 0 0 0 3 206 4 0 0 0 + 6 3 407 407 0 + 0 0 0 0 0 +# +OH 8 0 0 0 2 6 0 0 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +OH 8 0 0 0 2 15 0 0 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +OS 8 0 0 0 2 6 0 0 0 0 + 6 0 0 0 0 + 0 0 0 0 0 +# +OS 8 0 0 0 2 6 0 0 0 0 + 15 4 8 8 0 + 0 0 0 0 0 +# +OS 8 0 0 0 2 15 4 8 8 0 + 15 4 8 8 0 + 0 0 0 0 0 +# +O 8 0 0 0 1 6 3 7 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +O2 8 0 0 0 1 6 3 1808 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +O2 8 0 0 0 1 15 4 1808 1808 0 + 0 0 0 0 0 + 0 0 0 0 0 +# carboxylic acids COOH have types C O OH HO +# +O 8 0 0 0 1 6 3 6 208 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +O 8 0 0 0 1 6 3 6 2008 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +OW 8 0 0 0 2 1 1 0 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +P 15 0 0 0 4 8 0 0 0 0 + 8 0 0 0 0 + 8 0 0 0 0 +# +S 16 0 0 0 2 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +SH 16 0 0 0 2 1 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +SH 16 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CL 17 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +End \ No newline at end of file diff --git a/src/data/amber_s/amber95.par b/src/data/amber_s/amber95.par new file mode 100644 index 0000000..a145c77 --- /dev/null +++ b/src/data/amber_s/amber95.par @@ -0,0 +1,878 @@ +# +# This is the AMBER96 standard parameter file for NWChem 3.3 +# +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +# +Atoms +BR 79.90000 0.00000E+00 0.00000E+00 1 1111111111 + 35 0.00000E+00 0.00000E+00 +C 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CA 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CB 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CC 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CK 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CM 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CN 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CQ 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CR 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CT 12.01000 4.57729E-01 1.90800E-01 1 1111111111 + 6 2.28864E-01 1.90800E-01 +CV 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +CW 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +C* 12.01000 3.59824E-01 1.90800E-01 1 1111111111 + 6 1.79912E-01 1.90800E-01 +C0 40.08000 0.00000E+00 0.00000E+00 1 1111111111 + 6 0.00000E+00 0.00000E+00 +F 19.00000 2.55224E-01 1.75000E-01 1 1111111111 + 9 1.27612E-01 1.75000E-01 +H 1.00800 6.56887E-02 6.00000E-02 1 1111111111 + 1 3.28444E-02 6.00000E-02 +HC 1.00800 6.56887E-02 1.48700E-01 1 1111111111 + 1 3.28444E-02 1.48700E-01 +H1 1.00800 6.56887E-02 1.38700E-01 1 1111111111 + 1 3.28444E-02 1.38700E-01 +H2 1.00800 6.56887E-02 1.28700E-01 1 1111111111 + 1 3.28444E-02 1.28700E-01 +H3 1.00800 6.56887E-02 1.18700E-01 1 1111111111 + 1 3.28444E-02 1.18700E-01 +HA 1.00800 6.27598E-02 1.45900E-01 1 1111111111 + 1 3.13799E-02 1.45900E-01 +H4 1.00800 6.27598E-02 1.40900E-01 1 1111111111 + 1 3.13799E-02 1.40900E-01 +H5 1.00800 6.27598E-02 1.35900E-01 1 1111111111 + 1 3.13799E-02 1.35900E-01 +HO 1.00800 0.00000E+00 0.00000E+00 1 1111111111 + 1 0.00000E+00 0.00000E+00 +HS 1.00800 6.56887E-02 6.00000E-02 1 1111111111 + 1 3.28444E-02 6.00000E-02 +HW 1.00800 0.00000E+00 0.00000E+00 1 1111111111 + 1 0.00000E+00 0.00000E+00 +HP 1.00800 6.56887E-02 1.10000E-01 1 1111111111 + 1 3.28444E-02 1.10000E-01 +I 126.90000 1.67361E+00 2.35000E-01 1 1111111111 + 53 8.36805E-01 2.35000E-01 +IM 35.45000 4.18399E-01 2.47000E-01 1 1111111111 + 17 2.09200E-01 2.47000E-01 +IP 22.99000 1.15896E-02 1.86800E-01 1 1111111111 + 11 5.79480E-03 1.86800E-01 +IB 131.00000 4.18399E-01 5.00000E-01 1 1111111111 + 54 2.09200E-01 5.00000E-01 +N 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NA 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NB 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +NC 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +N2 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +N3 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +N* 14.01000 7.11280E-01 1.82400E-01 1 1111111111 + 7 3.55640E-01 1.82400E-01 +O 16.00000 8.78640E-01 1.66120E-01 1 1111111111 + 8 4.39320E-01 1.66120E-01 +OW 16.00000 6.35968E-01 1.76830E-01 1 1111111111 + 8 3.17984E-01 1.76830E-01 +OH 16.00000 8.80313E-01 1.72100E-01 1 1111111111 + 8 4.40157E-01 1.72100E-01 +OS 16.00000 7.11280E-01 1.68370E-01 1 1111111111 + 8 3.55640E-01 1.68370E-01 +O2 16.00000 8.78640E-01 1.66120E-01 1 1111111111 + 8 4.39320E-01 1.66120E-01 +P 30.97000 8.36800E-01 2.10000E-01 1 1111111111 + 15 4.18400E-01 2.10000E-01 +S 32.06000 1.04600E+00 2.00000E-01 1 1111111111 + 16 5.23000E-01 2.00000E-01 +SH 32.06000 1.04600E+00 2.00000E-01 1 1111111111 + 16 5.23000E-01 2.00000E-01 +# +Cross +# +Bonds +HW -OW 0.09570 4.62750E+05 +HW -HW 0.15130 4.62750E+05 +C -CA 0.14090 3.92459E+05 +C -CB 0.14190 3.74050E+05 +C -CM 0.14440 3.43088E+05 +C -CT 0.15220 2.65266E+05 +C -N* 0.13830 3.54803E+05 0.070000 +C -NA 0.13880 3.49782E+05 0.070000 +C -NC 0.13580 3.82418E+05 0.070000 +C -O 0.12290 4.76976E+05 0.570000 +C -O2 0.12500 5.48941E+05 0.570000 +C -OH 0.13640 3.76560E+05 0.300000 +CA -CA 0.14000 3.92459E+05 +CA -CB 0.14040 3.92459E+05 +CA -CM 0.14330 3.57314E+05 +CA -CT 0.15100 2.65266E+05 +CA -HA 0.10800 3.07106E+05 -0.050000 +CA -H4 0.10800 3.07106E+05 -0.050000 +CA -N2 0.13400 4.02501E+05 0.070000 +CA -NA 0.13810 3.57314E+05 0.070000 +CA -NC 0.13390 4.04174E+05 0.070000 +CB -CB 0.13700 4.35136E+05 +CB -N* 0.13740 3.64845E+05 0.070000 +CB -NB 0.13910 3.46435E+05 0.070000 +CB -NC 0.13540 3.85765E+05 0.070000 +CK -H5 0.10800 3.07106E+05 -0.050000 +CK -N* 0.13710 3.68192E+05 0.070000 +CK -NB 0.13040 4.42667E+05 0.070000 +CM -CM 0.13500 4.59403E+05 +CM -CT 0.15100 2.65266E+05 +CM -HA 0.10800 3.07106E+05 -0.050000 +CM -H4 0.10800 3.07106E+05 -0.050000 +CM -H5 0.10800 3.07106E+05 -0.050000 +CM -N* 0.13650 3.74886E+05 0.070000 +CQ -H5 0.10800 3.07106E+05 -0.050000 +CQ -NC 0.13240 4.20074E+05 0.070000 +CT -CT 0.15260 2.59408E+05 +CT -HC 0.10900 2.84512E+05 -0.050000 +CT -H1 0.10900 2.84512E+05 -0.050000 +CT -H2 0.10900 2.84512E+05 -0.050000 +CT -H3 0.10900 2.84512E+05 -0.050000 +CT -HP 0.10900 2.84512E+05 -0.050000 +CT -N* 0.14750 2.82002E+05 0.070000 +CT -N2 0.14630 2.82002E+05 0.070000 +CT -OH 0.14100 2.67776E+05 0.300000 +CT -OS 0.14100 2.67776E+05 0.300000 +H -N2 0.10100 3.63171E+05 0.270000 +H -N* 0.10100 3.63171E+05 0.270000 +H -NA 0.10100 3.63171E+05 0.270000 +HO -OH 0.09600 4.62750E+05 0.190000 +HO -OS 0.09600 4.62750E+05 0.190000 +O2 -P 0.14800 4.39320E+05 +OH -P 0.16100 1.92464E+05 +OS -P 0.16100 1.92464E+05 +C* -HC 0.10800 3.07106E+05 -0.050000 +C -N 0.13350 4.10032E+05 0.070000 +C* -CB 0.14590 3.24678E+05 +C* -CT 0.14950 2.65266E+05 +C* -CW 0.13520 4.56893E+05 +CA -CN 0.14000 3.92459E+05 +CB -CN 0.14190 3.74050E+05 +CC -CT 0.15040 2.65266E+05 +CC -CV 0.13750 4.28442E+05 +CC -CW 0.13710 4.33462E+05 +CC -NA 0.13850 3.53130E+05 0.070000 +CC -NB 0.13940 3.43088E+05 0.070000 +CN -NA 0.13800 3.58150E+05 0.070000 +CR -H5 0.10800 3.07106E+05 -0.050000 +CR -NA 0.13430 3.99154E+05 0.070000 +CR -NB 0.13350 4.08358E+05 0.070000 +CT -N 0.14490 2.82002E+05 0.070000 +CT -N3 0.14710 3.07106E+05 0.070000 +CT -S 0.18100 1.89954E+05 0.110000 +CT -SH 0.18100 1.98322E+05 0.110000 +CV -H4 0.10800 3.07106E+05 -0.050000 +CV -NB 0.13940 3.43088E+05 0.070000 +CW -H4 0.10800 3.07106E+05 -0.050000 +CW -NA 0.13810 3.57314E+05 0.070000 +H -N 0.10100 3.63171E+05 0.270000 +H -N3 0.10100 3.63171E+05 0.270000 +HS -SH 0.13360 2.29283E+05 0.190000 +S -S 0.20380 1.38909E+05 +CT -F 0.13800 3.07106E+05 +# +Angles +HW -OW -HW 1.82422 8.36800E+02 +HW -HW -OW 2.22948 0.00000E+00 +CB -C -NA 1.94255 5.85760E+02 +CB -C -O 2.24798 6.69440E+02 +CM -C -NA 1.99142 5.85760E+02 +CM -C -O 2.18690 6.69440E+02 +CT -C -O 2.10138 6.69440E+02 +CT -C -O2 2.04204 5.85760E+02 +CT -C -OH 2.04204 5.85760E+02 +N* -C -NA 2.01411 5.85760E+02 +N* -C -NC 2.06996 5.85760E+02 +N* -C -O 2.11010 6.69440E+02 +NA -C -O 2.10487 6.69440E+02 +NC -C -O 2.13803 6.69440E+02 +CT -C -N 2.03505 5.85760E+02 +N -C -O 2.14501 6.69440E+02 +O -C -O 2.19911 6.69440E+02 +O2 -C -O2 2.19911 6.69440E+02 +O -C -OH 2.19911 6.69440E+02 +CA -C -CA 2.09440 5.27184E+02 +CA -C -OH 2.09440 5.85760E+02 +C -CA -CA 2.09440 5.27184E+02 +CA -CA -CA 2.09440 5.27184E+02 +CA -CA -CB 2.09440 5.27184E+02 +CA -CA -CT 2.09440 5.85760E+02 +CA -CA -HA 2.09440 2.92880E+02 +CA -CA -H4 2.09440 2.92880E+02 +CB -CA -HA 2.09440 2.92880E+02 +CB -CA -H4 2.09440 2.92880E+02 +CB -CA -N2 2.15548 5.85760E+02 +CB -CA -NC 2.04727 5.85760E+02 +CM -CA -N2 2.09614 5.85760E+02 +CM -CA -NC 2.12057 5.85760E+02 +N2 -CA -NA 2.02458 5.85760E+02 +N2 -CA -NC 2.08218 5.85760E+02 +NA -CA -NC 2.15199 5.85760E+02 +C -CA -HA 2.09440 2.92880E+02 +N2 -CA -N2 2.09440 5.85760E+02 +CN -CA -HA 2.09440 2.92880E+02 +CA -CA -CN 2.09440 5.27184E+02 +C -CB -CB 2.08043 5.27184E+02 +C -CB -NB 2.26893 5.85760E+02 +CA -CB -CB 2.04727 5.27184E+02 +CA -CB -NB 2.31082 5.85760E+02 +CB -CB -N* 1.85354 5.85760E+02 +CB -CB -NB 1.92684 5.85760E+02 +CB -CB -NC 2.22879 5.85760E+02 +N* -CB -NC 2.20261 5.85760E+02 +C* -CB -CA 2.35445 5.27184E+02 +C* -CB -CN 1.89892 5.27184E+02 +CA -CB -CN 2.02807 5.27184E+02 +H5 -CK -N* 2.14763 2.92880E+02 +H5 -CK -NB 2.14763 2.92880E+02 +N* -CK -NB 1.98793 5.85760E+02 +C -CM -CM 2.10661 5.27184E+02 +C -CM -CT 2.08916 5.85760E+02 +C -CM -HA 2.08916 2.92880E+02 +C -CM -H4 2.08916 2.92880E+02 +CA -CM -CM 2.04204 5.27184E+02 +CA -CM -HA 2.15199 2.92880E+02 +CA -CM -H4 2.15199 2.92880E+02 +CM -CM -CT 2.08916 5.85760E+02 +CM -CM -HA 2.08916 2.92880E+02 +CM -CM -H4 2.08916 2.92880E+02 +CM -CM -N* 2.11534 5.85760E+02 +H4 -CM -N* 2.07869 2.92880E+02 +H5 -CQ -NC 2.01498 2.92880E+02 +NC -CQ -NC 2.25322 5.85760E+02 +CM -CT -HC 1.91114 4.18400E+02 +CT -CT -CT 1.91114 3.34720E+02 +CT -CT -HC 1.91114 4.18400E+02 +CT -CT -H1 1.91114 4.18400E+02 +CT -CT -H2 1.91114 4.18400E+02 +CT -CT -HP 1.91114 4.18400E+02 +CT -CT -N* 1.91114 4.18400E+02 +CT -CT -OH 1.91114 4.18400E+02 +CT -CT -OS 1.91114 4.18400E+02 +HC -CT -HC 1.91114 2.92880E+02 +H1 -CT -H1 1.91114 2.92880E+02 +HP -CT -HP 1.91114 2.92880E+02 +H2 -CT -N* 1.91114 4.18400E+02 +H1 -CT -N* 1.91114 4.18400E+02 +H1 -CT -OH 1.91114 4.18400E+02 +H1 -CT -OS 1.91114 4.18400E+02 +H2 -CT -OS 1.91114 4.18400E+02 +N* -CT -OS 1.91114 4.18400E+02 +H1 -CT -N 1.91114 4.18400E+02 +C -CT -H1 1.91114 4.18400E+02 +C -CT -HP 1.91114 4.18400E+02 +H1 -CT -S 1.91114 4.18400E+02 +H1 -CT -SH 1.91114 4.18400E+02 +CT -CT -S 2.00189 4.18400E+02 +CT -CT -SH 1.89543 4.18400E+02 +H2 -CT -H2 1.91114 2.92880E+02 +H1 -CT -N2 1.91114 4.18400E+02 +HP -CT -N3 1.91114 4.18400E+02 +CA -CT -CT 1.98968 5.27184E+02 +C -CT -HC 1.91114 4.18400E+02 +C -CT -N 1.92161 5.27184E+02 +CT -CT -N2 1.94081 6.69440E+02 +CT -CT -N 1.91463 6.69440E+02 +C -CT -CT 1.93906 5.27184E+02 +CA -CT -HC 1.91114 4.18400E+02 +CT -CT -N3 1.94081 6.69440E+02 +CC -CT -CT 1.97397 5.27184E+02 +CC -CT -HC 1.91114 4.18400E+02 +C -CT -N3 1.94081 6.69440E+02 +C* -CT -CT 2.01760 5.27184E+02 +C* -CT -HC 1.91114 4.18400E+02 +CT -CC -NA 2.09440 5.85760E+02 +CT -CC -CV 2.09440 5.85760E+02 +CT -CC -NB 2.09440 5.85760E+02 +CV -CC -NA 2.09440 5.85760E+02 +CW -CC -NA 2.09440 5.85760E+02 +CW -CC -NB 2.09440 5.85760E+02 +CT -CC -CW 2.09440 5.85760E+02 +H5 -CR -NA 2.09440 2.92880E+02 +H5 -CR -NB 2.09440 2.92880E+02 +NA -CR -NA 2.09440 5.85760E+02 +NA -CR -NB 2.09440 5.85760E+02 +CC -CV -H4 2.09440 2.92880E+02 +CC -CV -NB 2.09440 5.85760E+02 +H4 -CV -NB 2.09440 2.92880E+02 +CC -CW -H4 2.09440 2.92880E+02 +CC -CW -NA 2.09440 5.85760E+02 +H4 -CW -NA 2.09440 2.92880E+02 +C* -CW -H4 2.09440 2.92880E+02 +C* -CW -NA 1.89717 5.85760E+02 +CT -C* -CW 2.18166 5.85760E+02 +CB -C* -CT 2.24449 5.85760E+02 +CB -C* -CW 1.85703 5.27184E+02 +CA -CN -NA 2.31780 5.85760E+02 +CB -CN -NA 1.82212 5.85760E+02 +CA -CN -CB 2.14152 5.27184E+02 +C -N -CT 2.12756 4.18400E+02 +C -N -H 2.09440 2.51040E+02 +CT -N -H 2.06019 2.51040E+02 +CT -N -CT 2.05949 4.18400E+02 +H -N -H 2.09440 2.92880E+02 +C -N* -CM 2.12232 5.85760E+02 +C -N* -CT 2.05251 5.85760E+02 +C -N* -H 2.08043 2.51040E+02 +CB -N* -CK 1.83958 5.85760E+02 +CB -N* -CT 2.19562 5.85760E+02 +CB -N* -H 2.19562 2.51040E+02 +CK -N* -CT 2.24798 5.85760E+02 +CK -N* -H 2.24798 2.51040E+02 +CM -N* -CT 2.11534 5.85760E+02 +CM -N* -H 2.11534 2.51040E+02 +CA -N2 -H 2.09440 2.92880E+02 +H -N2 -H 2.09440 2.92880E+02 +CT -N2 -H 2.06647 2.92880E+02 +CA -N2 -CT 2.15025 4.18400E+02 +CT -N3 -H 1.91114 4.18400E+02 +CT -N3 -CT 1.91114 4.18400E+02 +H -N3 -H 1.91114 2.92880E+02 +C -NA -C 2.20610 5.85760E+02 +C -NA -CA 2.18515 5.85760E+02 +C -NA -H 2.03854 2.51040E+02 +CA -NA -H 2.05949 2.51040E+02 +CC -NA -CR 2.09440 5.85760E+02 +CC -NA -H 2.09440 2.51040E+02 +CR -NA -CW 2.09440 5.85760E+02 +CR -NA -H 2.09440 2.51040E+02 +CW -NA -H 2.09440 2.51040E+02 +CN -NA -CW 1.94779 5.85760E+02 +CN -NA -H 2.14850 2.51040E+02 +CB -NB -CK 1.81165 5.85760E+02 +CC -NB -CR 2.04204 5.85760E+02 +CR -NB -CV 2.04204 5.85760E+02 +C -NC -CA 2.10312 5.85760E+02 +CA -NC -CB 1.95826 5.85760E+02 +CA -NC -CQ 2.06996 5.85760E+02 +CB -NC -CQ 1.93732 5.85760E+02 +C -OH -HO 1.97222 2.92880E+02 +CT -OH -HO 1.89368 4.60240E+02 +HO -OH -P 1.89368 3.76560E+02 +CT -OS -CT 1.91114 5.02080E+02 +CT -OS -P 2.10312 8.36800E+02 +P -OS -P 2.10312 8.36800E+02 +O2 -P -OH 1.88897 3.76560E+02 +O2 -P -O2 2.09265 1.17152E+03 +O2 -P -OS 1.88897 8.36800E+02 +OH -P -OS 1.79071 3.76560E+02 +OS -P -OS 1.79071 3.76560E+02 +CT -S -CT 1.72613 5.18816E+02 +CT -S -S 1.80991 5.69024E+02 +CT -SH -HS 1.67552 3.59824E+02 +HS -SH -HS 1.60692 2.92880E+02 +F -CT -F 1.90415 6.44336E+02 +F -CT -H1 1.91114 2.92880E+02 +# +Proper dihedrals + -C -CA - 3.14159 1.51670E+01 2 + -C -CB - 3.14159 1.25520E+01 2 + -C -CM - 3.14159 9.10020E+00 2 + -C -N* - 3.14159 6.06680E+00 2 + -C -NA - 3.14159 5.64840E+00 2 + -C -NC - 3.14159 1.67360E+01 2 + -C -OH - 3.14159 3.76560E+00 2 + -C -CT - 0.00000 0.00000E+00 2 + -CA -CA - 3.14159 1.51670E+01 2 + -CA -CB - 3.14159 1.46440E+01 2 + -CA -CM - 3.14159 1.06692E+01 2 + -CA -CT - 0.00000 0.00000E+00 2 + -CA -N2 - 3.14159 1.00416E+01 2 + -CA -NA - 3.14159 6.27600E+00 2 + -CA -NC - 3.14159 2.00832E+01 2 + -CB -CB - 3.14159 2.28028E+01 2 + -CB -N* - 3.14159 6.90360E+00 2 + -CB -NB - 3.14159 1.06692E+01 2 + -CB -NC - 3.14159 1.73636E+01 2 + -CK -N* - 3.14159 7.11280E+00 2 + -CK -NB - 3.14159 4.18400E+01 2 + -CM -CM - 3.14159 2.78236E+01 2 + -CM -CT - 0.00000 0.00000E+00 3 + -CM -N* - 3.14159 7.74040E+00 2 + -CQ -NC - 3.14159 2.84512E+01 2 + -CT -CT - 0.00000 6.50844E-01 3 + -CT -N - 0.00000 0.00000E+00 2 + -CT -N* - 0.00000 0.00000E+00 2 + -CT -N2 - 0.00000 0.00000E+00 3 + -CT -OH - 0.00000 6.97333E-01 3 + -CT -OS - 0.00000 1.60387E+00 3 + -OH -P - 0.00000 1.04600E+00 3 + -OS -P - 0.00000 1.04600E+00 3 + -C -N - 3.14159 1.04600E+01 2 + -CT -N3 - 0.00000 6.50844E-01 3 + -CT -S - 0.00000 1.39467E+00 3 + -CT -SH - 0.00000 1.04600E+00 3 + -C* -CB - 3.14159 7.00820E+00 2 + -C* -CT - 0.00000 0.00000E+00 2 + -C* -CW - 3.14159 2.73006E+01 2 + -CA -CN - 3.14159 1.51670E+01 2 + -CB -CN - 3.14159 1.25520E+01 2 + -CC -CT - 0.00000 0.00000E+00 2 + -CC -CV - 3.14159 2.15476E+01 2 + -CC -CW - 3.14159 2.24890E+01 2 + -CC -NA - 3.14159 5.85760E+00 2 + -CC -NB - 3.14159 1.00416E+01 2 + -CN -NA - 3.14159 6.38060E+00 2 + -CR -NA - 3.14159 9.72780E+00 2 + -CR -NB - 3.14159 2.09200E+01 2 + -CV -NB - 3.14159 1.00416E+01 2 + -CW -NA - 3.14159 6.27600E+00 2 +CT -CT -OS -CT 0.00000 1.60247E+00 -3 +CT -CT -OS -CT 3.14159 4.18400E-01 2 +C -CT -N -C 3.14159 1.25520E+00 -2 +C -CT -N -C 0.00000 3.55640E+00 1 +N -C -CT -N 3.14159 1.25520E+00 -2 +N -C -CT -N 0.00000 3.55640E+00 1 +CT -CT -N -C 3.14159 2.09200E+00 -4 +CT -CT -N -C 3.14159 6.27600E-01 -3 +CT -CT -N -C 0.00000 2.21752E+00 1 +N -C -CT -CT 0.00000 4.18400E-01 -4 +N -C -CT -CT 0.00000 2.92880E-01 2 +O -C -N -H 3.14159 1.04600E+01 -2 +O -C -N -H 0.00000 8.36800E+00 1 +CT -S -S -CT 0.00000 1.46440E+01 -2 +CT -S -S -CT 0.00000 2.51040E+00 3 +OS -CT -CT -OS 0.00000 6.02496E-01 -3 +OS -CT -CT -OS 0.00000 4.18400E+00 2 +OS -CT -CT -OH 0.00000 6.02496E-01 -3 +OS -CT -CT -OH 0.00000 4.18400E+00 2 +OH -CT -CT -OH 0.00000 6.02496E-01 -3 +OH -CT -CT -OH 0.00000 4.18400E+00 2 +CT -OS -P -OH 0.00000 1.04600E+00 -3 +CT -OS -P -OH 0.00000 5.02080E+00 2 +CT -OS -P -OS 0.00000 1.04600E+00 -3 +CT -OS -P -OS 0.00000 5.02080E+00 2 +OS -CT -N* -CK 3.14159 2.09200E+00 -2 +OS -CT -N* -CK 0.00000 1.04600E+01 1 +OS -CT -N* -CM 3.14159 2.09200E+00 -2 +OS -CT -N* -CM 0.00000 1.04600E+01 1 +# +Improper dihedrals + - -C -O 3.14159 4.39320E+01 2 + -O2 -C -O2 3.14159 4.39320E+01 2 + - -N -H 3.14159 4.18400E+00 2 + - -N2 -H 3.14159 4.18400E+00 2 + - -NA -H 3.14159 4.18400E+00 2 + -N2 -CA -N2 3.14159 4.39320E+01 2 + -CT -N -CT 3.14159 4.18400E+00 2 + - -CA -HA 3.14159 4.60240E+00 2 + - -CW -H4 3.14159 4.60240E+00 2 + - -CR -H5 3.14159 4.60240E+00 2 + - -CV -H4 3.14159 4.60240E+00 2 + - -CQ -H5 3.14159 4.60240E+00 2 + - -CK -H5 3.14159 4.60240E+00 2 + - -CM -H4 3.14159 4.60240E+00 2 + - -CM -HA 3.14159 4.60240E+00 2 + - -CA -H4 3.14159 4.60240E+00 2 + - -CA -H5 3.14159 4.60240E+00 2 +CK -CB -N* -CT 3.14159 4.18400E+00 2 +CM -C -N* -CT 3.14159 4.18400E+00 2 +CM -C -CM -CT 3.14159 4.60240E+00 2 +CT -O -C -OH 3.14159 4.39320E+01 2 +NA -CV -CC -CT 3.14159 4.60240E+00 2 +NB -CW -CC -CT 3.14159 4.60240E+00 2 +NA -CW -CC -CT 3.14159 4.60240E+00 2 +CW -CB -C* -CT 3.14159 4.60240E+00 2 +CA -CA -CA -CT 3.14159 4.60240E+00 2 +C -CM -CM -CT 3.14159 4.60240E+00 2 +NC -CM -CA -N2 3.14159 4.60240E+00 2 +CB -NC -CA -N2 3.14159 4.60240E+00 2 +NA -NC -CA -N2 3.14159 4.60240E+00 2 +CA -CA -C -OH 3.14159 4.60240E+00 2 +# +Atom types +# +# Definition of the atom types +# +# This file contains the definition of AMBER atom types in terms of number and +# type of neighbor atoms. +# +# Note that the order in which the definitions are given is important. +# For each atom the last applicable entry in this file will be used, i.e. +# atom type definitions are given in increasing specificity. +# +# Atomic number increased by 200 means singly protonated +# 400 doubly +# 600 triply +# 800 un-protonated +# 1000 one non-hydrogen +# 2000 two non-hydrogens +# 3000 three non-hydrogens +# 4000 four non-hydrogens +# +# Atom number 3500 would signify any unprotonated atom with three non-hydrogens +# +# +# Each entry contains: +# +# 1 a4 atom type name +# +# 2 i7 atomic number +# +# 3 i3 atom saturation : 0 = undetermined, always applies +# 1 = aliphatic; +# 2 = double bond; +# 3 = aromatic; +# +# 4 i5 aliphatic ring : -1 = not in aliphatic ring +# 0 = any +# 1 = in at least one aliphatic ring +# 3 = in 3-membered aliphatic ring +# 4 = in 4-membered aliphatic ring +# 5 = in 5-membered aliphatic ring +# 6 = in 6-membered aliphatic ring +# 56 = junction 5 & 6 membered aliphatic rings +# 66 = junction two 6 membered aliphatic rings +# +# 5 i5 aromatic ring : -1 = not in aromatic ring +# 0 = any +# 1 = in at least one aromatic ring +# 5 = in 5-membered aromatic ring +# 6 = in 6-membered aromatic ring +# 56 = junction 5 & 6 membered aromatic rings +# 66 = junction two 6 membered aromatic rings +# 666 = junction three 6 membered aromatic rings +# +# 6 i3 number of neighbors : -1 = no neighbors +# 0 = any number of neighbors +# +# 7 i7 atom num neighbor 1 +# +# 8 i3 num n1 neighbors 0 = any number of neighbors +# +# 9 i7 atom num neighb n11 +# +# 10 i7 atom num neighb n12 +# +# 11 i7 atom num neighb n13 +# +# 12 i7 atom num neighbor 2 +# +# 13 i3 num n2 neighbors 0 = any number of neighbors +# +# 14 i7 atom num neighb n21 +# +# 15 i7 atom num neighb n22 +# +# 16 i7 atom num neighb n23 +# +# 17 i7 atom num neighbor 3 +# +# 18 i3 num n3 neighbors 0 = any number of neighbors +# +# 19 i7 atom num neighb n31 +# +# 20 i7 atom num neighb n32 +# +# 21 i7 atom num neighb n33 +# +# +# +# 1 2 3 4 5 +#23456789 123456789 123456789 123456789 123456789 12345678 +# 1 2 3 4 5 6 7 8 9 10 11 +# 12 13 14 15 16 +# 17 18 19 20 21 +# +H 1 0 0 0 1 7 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HO 1 0 0 0 1 208 2 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HS 1 0 0 0 1 16 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HA 1 0 0 0 1 6 3 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HC 1 0 0 0 1 6 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H1 1 0 0 0 1 6 4 7 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H1 1 0 0 0 1 6 4 8 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H1 1 0 0 0 1 6 4 16 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H2 1 0 0 0 1 6 4 7 7 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H2 1 0 0 0 1 6 4 7 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H2 1 0 0 0 1 6 4 8 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 7 7 7 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 7 7 8 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 7 8 8 + 0 0 0 0 0 + 0 0 0 0 0 +# +H3 1 0 0 0 1 6 4 8 8 8 + 0 0 0 0 0 + 0 0 0 0 0 +# +HP 1 0 0 0 1 6 4 607 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HP 1 0 0 0 1 6 4 1407 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H4 1 0 0 0 1 6 3 7 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H4 1 0 0 0 1 6 3 8 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H5 1 0 0 0 1 6 3 7 7 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H5 1 0 0 0 1 6 3 7 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +H5 1 0 0 0 1 6 3 8 8 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +HW 1 0 0 0 1 408 2 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CT 6 0 0 0 4 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CA 6 2 0 0 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# CZ in arginine +# +CA 6 0 0 0 3 207 3 0 0 0 + 407 3 0 0 0 + 407 3 0 0 0 +# +# aromatic carbon in 6-membered ring +# +CA 6 0 0 6 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CM 6 2 0 0 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +CM 6 3 0 0 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# +C 6 0 0 0 3 8 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CV 6 0 0 5 3 6 0 0 0 0 + 7 2 0 0 0 + 0 0 0 0 0 +# +CB 6 0 0 56 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CR 6 0 0 5 3 7 0 0 0 0 + 7 0 0 0 0 + 0 0 0 0 0 +# +CK 6 0 0 5 3 807 3 0 0 0 + 7 0 0 0 0 + 0 0 0 0 0 +# +CW 6 0 0 5 3 6 0 0 0 0 + 207 0 0 0 0 + 0 0 0 0 0 +# +C* 6 0 0 5 3 6 0 0 0 0 + 6 0 0 0 0 + 0 0 0 0 0 +# +CC 806 0 0 5 3 7 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +CN 6 0 0 56 3 206 0 0 0 0 + 207 0 0 0 0 + 0 0 0 0 0 +# +CQ 6 0 0 6 3 7 2 0 0 0 + 7 2 0 0 0 + 0 0 0 0 0 +# +# guanidinium ion +# +N2 7 0 0 0 3 6 3 7 7 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# aromatic amine +# +N2 7 0 0 0 3 6 3 0 0 0 + 1 1 0 0 0 + 1 1 0 0 0 +# +N2 7 0 0 0 3 6 3 0 0 0 + 6 3 0 0 0 + 0 0 0 0 0 +# +N 7 0 0 0 3 6 3 8 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +# proline +# +N 7 0 0 0 3 6 3 8 6 0 + 6 4 6 6 1 + 6 4 6 1 1 +# +NA 207 0 0 5 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +NA 207 0 0 6 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +NB 7 0 0 5 2 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +NC 7 0 0 6 2 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N* 7 0 0 5 3 6 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N* 7 0 0 6 3 6 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N3 7 0 0 0 4 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +# NE in arginine +# +N2 7 0 0 0 3 206 4 0 0 0 + 6 3 407 407 0 + 0 0 0 0 0 +# +OH 8 0 0 0 2 6 0 0 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +OH 8 0 0 0 2 15 0 0 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +OS 8 0 0 0 2 6 0 0 0 0 + 6 0 0 0 0 + 0 0 0 0 0 +# +OS 8 0 0 0 2 6 0 0 0 0 + 15 4 8 8 0 + 0 0 0 0 0 +# +OS 8 0 0 0 2 15 4 8 8 0 + 15 4 8 8 0 + 0 0 0 0 0 +# +O 8 0 0 0 1 6 3 7 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +O2 8 0 0 0 1 6 3 1808 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +O2 8 0 0 0 1 15 4 1808 1808 0 + 0 0 0 0 0 + 0 0 0 0 0 +# carboxylic acids COOH have types C O OH HO +# +O 8 0 0 0 1 6 3 6 208 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +O 8 0 0 0 1 6 3 6 2008 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +OW 8 0 0 0 2 1 1 0 0 0 + 1 1 0 0 0 + 0 0 0 0 0 +# +P 15 0 0 0 4 8 0 0 0 0 + 8 0 0 0 0 + 8 0 0 0 0 +# +S 16 0 0 0 2 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +SH 16 0 0 0 2 1 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +SH 16 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Cl 17 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +End \ No newline at end of file diff --git a/src/data/amber_t/amber.par b/src/data/amber_t/amber.par new file mode 100644 index 0000000..9864474 --- /dev/null +++ b/src/data/amber_t/amber.par @@ -0,0 +1,268 @@ +This is the AMBER96 user defined parameter file for NWChem 3.2 and ARGOS 7.0 +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +CD 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +CY 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +CX 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +NO 14.00674 7.11283E-01 1.82400E-01 1 1111111111 + 7 3.55641E-01 1.82400E-01 +NP 14.00674 7.11283E-01 1.82400E-01 1 1111111111 + 7 3.55641E-01 1.82400E-01 +N4 14.00674 3.35276E-03 1.98770E-03 1 1111111111 + 7 1.67638E-03 1.98770E-03 +CU 12.01100 2.03050E-03 1.93200E-03 1 1111111111 + 6 1.01525E-03 1.93200E-03 +H9 1.00790 1.22578E-04 1.72992E-04 1 1111111111 + 1 6.12890E-05 1.72992E-04 +FE 55.00000 0.00000E+00 0.00000E+00 1 1111111111 + 26 0.00000E+00 0.00000E+00 +MG 24.30500 4.18399E-01 1.17000E-01 1 1111111111 + 12 2.09200E-01 1.17000E-01 +ZN 65.38000 0.00000E+00 0.00000E+00 1 1111111111 + 30 0.00000E+00 0.00000E+00 +HWS 1.00800 6.56887E-02 6.00000E-02 1 1111111111 + Q 1 3.28444E-02 6.00000E-02 +HO 1.00800 6.56887E-02 6.00000E-02 1 1111111111 + Q 1 3.28444E-02 6.00000E-02 +OWS 15.99940 7.11280E-01 1.68370E-01 1 1111111111 + Q 8 3.55640E-01 1.68370E-01 +OH 15.99940 7.11280E-01 1.68370E-01 1 1111111111 + Q 8 3.55640E-01 1.68370E-01 +CL 35.45300 1.99247E+00 1.76561E-01 1 1111111111 + 17 9.96235E-01 1.76561E-01 +Ne 20.17900 3.16779E-01 1.55006E-01 1 1111111111 + 10 1.58389E-01 1.55006E-01 +Li 6.94000 6.18572E-02 1.44006E-01 1 1111111111 + 3 3.09286E-02 1.44006E-01 +Na 22.98977 6.18572E-02 1.44006E-01 1 1111111111 + 11 3.09286E-02 1.44006E-01 +Mg 24.30500 4.30952E-02 1.36000E-01 1 1111111111 + 12 2.15476E-02 1.36000E-01 +K 39.10000 1.37235E-03 2.65800E-01 1 1111111111 + 19 6.86175E-04 2.65800E-01 +Ca 40.08000 3.78520E-02 1.74000E-01 1 1111111111 + 20 1.89260E-02 1.74000E-01 +Rb 85.47000 7.11278E-04 2.95600E-01 1 1111111111 + 37 3.55639E-04 2.95600E-01 +Sr 87.62000 2.70286E-01 1.92000E-01 1 1111111111 + 38 1.35143E-01 1.92000E-01 +Cs 132.91000 3.37229E-04 3.39500E-01 1 1111111111 + 55 1.68614E-04 3.39500E-01 +Cl 35.45300 4.44950E-01 2.50000E-01 1 1111111111 + 17 2.22475E-01 2.50000E-01 +Cross +HC OWS 5.72430E-01 1.54315e-01 + 5.72430E-01 1.54315e-01 TPS000106 CPL 259, 142-145 (1996) +CT OWS 7.30585E-01 1.79759e-01 + 7.30585E-01 1.79759e-01 TPS000106 CPL 259, 142-145 (1996) +CL OWS 1.06686E-00 1.77110e-01 + 1.06686E-00 1.77110e-01 TPS000106 CPL 259, 142-145 (1996) +Bonds +HC -CD 0.10900 2.82838E+05 +HC -CX 0.10900 2.84512E+05 +HC -CY 0.10900 2.84512E+05 +CB -CC 0.14440 2.28446E+05 +CB -CT 0.15010 2.48530E+05 +CB -CY 0.15010 2.48530E+05 +CC -CD 0.13910 3.27189E+05 +CC -NO 0.13840 2.64429E+05 +CC -NP 0.13840 2.64429E+05 +CT -Cl 0.17720 1.31440E+05 +CX -CY 0.13400 4.76976E+05 +FE -NO 0.20100 4.18400E+04 +FE -NP 0.20100 4.18400E+04 +FE -S 0.15220 4.18400E+04 +ZN -S 0.15220 4.18400E+04 +CU -N4 0.14710 0.15355E+06 +CU -H9 0.10900 0.13849E+06 +AC -H2 0.10900 2.84512E+05 tps990729 copy CT-H2 +EC -H2 0.10900 2.84512E+05 tps990729 copy CT-H2 +C -OS 0.14100 2.67776E+05 tps990729 copy CT-OS +C -AC 0.15220 2.65266E+05 tps990729 copy C-CT +S -O2 0.14900 1.69566E+05 tps991219 for SO4-- taken from Smith +CL -CT 0.17720 0.13144E+06 +CW -CV 0.13750 4.28442E+05 +Angles +CB -CB -CC 1.86750 5.85760E+02 +CB -CB -CT 2.23751 5.85760E+02 +CB -CB -CY 2.23751 5.85760E+02 +CB -CC -CD 2.18864 5.85760E+02 +CB -CC -NO 1.92510 5.85760E+02 +CB -CC -NP 1.92510 5.85760E+02 +CD -CC -NO 2.19039 5.85760E+02 +CD -CC -NP 2.19039 5.85760E+02 +CC -CB -CT 2.17992 5.85760E+02 +CC -CB -CY 2.17992 5.85760E+02 +HC -CD -CC 2.05949 2.51040E+02 +CC -CD -CC 2.16595 5.85760E+02 +HC -CT -CB 1.91114 2.92880E+02 +CB -CT -CT 1.98968 5.27184E+02 +CT -CT -Cl 1.91986 3.55810E+02 +Cl -CT -Cl 1.94604 4.18600E+02 +HC -CX -HC 2.09440 2.92880E+02 +HC -CX -CY 2.09440 2.92880E+02 +HC -CY -CB 2.09440 2.92880E+02 +HC -CY -CX 2.09440 2.92880E+02 +CB -CY -CX 2.09440 5.85760E+02 +CC -NO -CC 1.83958 5.85760E+02 +CC -NO -FE 2.22355 2.51040E+02 +CC -NP -CC 1.83958 5.85760E+02 +CC -NP -FE 2.22355 2.51040E+02 +NB -FE -NO 1.57080 4.18400E+02 +NB -FE -NP 1.57080 4.18400E+02 +NO -FE -NO 1.57080 0.00000E+00 +NO -FE -NP 1.57080 4.18400E+02 +NP -FE -NP 1.57080 0.00000E+00 +CT -S -FE 2.19911 4.18400E+02 +CT -S -ZN 2.19911 4.18400E+02 +S -FE -S 2.19911 6.69440E+02 +S -ZN -S 2.19911 6.69440E+02 +H9 -CU -N4 1.91114 0.14644E+03 +CU -N4 -CU 1.97222 0.20920E+03 +H9 -CU -H9 1.91114 0.14644E+03 +H2 -AC -OS 1.91114 4.18400E+02 tps990729 copy H2-CT-OS +H2 -AC -OG 1.91114 4.18400E+02 tps990729 copy H2-CT-OS +H2 -EC -OG 1.91114 4.18400E+02 tps000315 copy H2-CT-OS +H2 -EC -OS 1.91114 4.18400E+02 tps980817 +OS -AC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-OS +OS -EC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-H2 +CT -AC -H2 1.91114 4.18400E+02 tps980817 +CT -EC -H2 1.91114 4.18400E+02 tps980817 +AC -CT -H1 1.91114 4.18400E+02 tps990729 copy CT-CT-H1 +EC -CT -H1 1.91114 4.18400E+02 tps980817 +AC -CT -N 1.91114 4.18400E+02 tps990729 copy CT-CT-N* +EC -CT -N 1.91114 4.18400E+02 tps980817 +CT -OS -C 1.91114 5.02080E+02 tps990729 copy CT-OS-CT +H1 -CT -OG 1.91114 4.18400E+02 tps990729 copy H1-CT-OS +CT -OG -CT 1.91114 5.02080E+02 tps990729 copy CT-OS-CT +AC -OS -P 2.10312 8.36800E+02 tps980817 copy CT-OS-P +EC -OS -P 2.10312 8.36800E+02 tps980817 +OS -C -O 2.19911 6.69440E+02 tps980817 +CT -C -OS 2.04204 5.85760E+02 tps980817 +AC -C -O 2.10138 6.69440E+02 tps990729 copy CT-C-O +AC -C -OH 2.04204 5.85760E+02 tps990729 copy CT-C-OH +C -AC -OG 1.91114 4.18400E+02 tps990729 copy CT-CT-OS +C -AC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-OS +C -AC -CT 1.93906 5.27184E+02 tps990729 copy C-CT-CT +OG -CT -C 1.91114 4.18400E+02 tps990729 copy OS-CT-CT +OS -CT -C 1.91114 4.18400E+02 tps990729 copy OS-CT-CT +OG -CT -OS 1.91114 4.18400E+02 tps990729 copy N*-CT-OS +AC -C -O2 2.04204 5.85760E+02 tps990729 copy CT-C-O2 +OS -C -O2 2.19911 6.69440E+02 tps990729 copy O2-C-O2 +O2 -S -O2 1.91114 4.18400E+02 tps991219 test +CT -S -O2 1.91114 4.18400E+02 tps991219 test +C -CT -OH 1.91114 4.18400E+02 tps000313 test +OS -C -N 2.03505 5.85760E+02 tps000313 test +CL -CT -CL 1.94604 0.41860E+03 TPS000106 CPL 259, 142-145 (1996) +CL -CT -CT 1.91986 0.35581E+03 TPS000106 CPL 259, 142-145 (1996) +CL -CT -HC 1.87797 0.21257E+03 +H1 -CT -N3 1.91114 4.18400E+02 +CV -CW -H4 2.09440 2.92880E+02 +CV -CW -NA 2.09440 5.85760E+02 +CW -CV -H4 2.09440 2.92880E+02 +CW -CV -NB 2.09440 5.85760E+02 +CT -CM -HA 2.09701 2.92880E+02 +CT -CM -CT 2.10487 5.85760E+02 +CM -CT -CM 1.91114 3.34720E+02 +CA -CT -CM 1.91114 3.34720E+02 +CM -CT -CT 1.91114 3.34720E+02 +NA -C -CA 2.00364 5.85760E+02 +O -C -CA 2.14152 5.85760E+02 +NA -CA -CA 2.09440 5.85760E+02 +NA -CA -CT 2.09440 5.85760E+02 +CA -CT -N3 1.94081 6.69440E+02 +CM -CT -N3 1.94081 6.69440E+02 +CT -AC -CT 1.91114 3.34720E+02 +Proper dihedrals + -NB -FE - 0.00000 0.00000E+02 2 + -NO -FE - 3.14159 0.00000E+02 2 + -NP -FE - 3.14159 0.00000E+02 2 + -CB -CC - 3.14159 3.29490E+00 2 + -CB -CT - 3.14159 0.00000E+00 2 + -CB -CY - 3.14159 0.00000E+00 2 + -CC -CD - 3.14159 8.26340E+00 2 + -CC -NO - 3.14159 5.96220E+00 2 + -CC -NP - 3.14159 5.96220E+00 2 + -CX -CY - 3.14159 3.13800E+01 2 + -CU -N4 - 0.00000 0.65084E+00 3 + -C -OS - 3.14159 6.06680E+00 2 tps990729 copy -C-N*- + -AC -OG - 0.00000 1.60387E+00 3 tps990729 copy -CT-OS- + -EC -OG - 0.00000 1.60387E+00 3 tps000315 copy -CT-OS- +C -AC -OG -CT 0.52360 1.58992E+00 -3 tps990729 copy CT-CT-OS-CT +C -AC -OG -CT 3.14159 4.18400E-01 2 tps990729 copy CT-CT-OS-CT + -C -AC - 0.00000 0.00000E+00 2 tps990729 copy -C-CT- +CL -CT -CT -CL 0.00000 1.15245E+00 3 +HC -CT -CT -HC 0.00000 0.82318E+00 3 + -CW -CV - 3.14159 2.15476E+01 2 + -CT -CT - 0.00000 6.04356E-01 3 +CT -CT -N -C 0.00000 0.00000E+00 1 +HC -CT -N -C 0.00000 0.00000E+00 1 +HC -CT -N -H 0.00000 0.00000E+00 1 +CT -CT -N -H 0.00000 0.00000E+00 1 +CT -EC -N -H 0.00000 0.00000E+00 1 +OH -CT -CT -OH 0.00000 5.60656E+00 -1 +OH -CT -CT -OH 3.14159-4.81160E+00 -2 +OH -CT -CT -OH 0.00000 3.22168E+00 3 +CT -EC -OH -HO 0.00000 6.97333E-01 3 +Improper dihedrals + - -CC -CC 3.14159 4.18400E+00 2 + - -CC -CB 3.14159 4.18400E+00 2 + - -CB -NP 3.14159 4.18400E+00 2 + - -CB -NO 3.14159 4.18400E+00 2 + - -CB -CY 3.14159 4.18400E+00 2 + - -CB -CT 3.14159 4.18400E+00 2 + - -CD -HC 3.14159 4.18400E+00 2 + -OS -C -O2 3.14159 4.39320E+01 2 tps990729 copy -O2-C-O2 +CA -NA -CA -CT 3.14159 4.60240E+00 2 +CT -CT -CM -CM 3.14159 4.60240E+00 2 +Atom types +# +O2 8 0 0 0 1 15 4 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N 7 0 0 0 3 1 0 0 0 0 + 15 4 0 0 0 + 15 4 0 0 0 +# +N3 7 0 0 0 3 6 4 0 0 0 + 6 4 0 0 0 + 6 4 0 0 0 +O2 8 0 0 0 1 16 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +S 16 0 0 0 4 8 0 0 0 0 + 8 0 0 0 0 + 8 0 0 0 0 +NB 7 0 0 0 3 1 0 0 0 0 + 6 3 7 1 0 + 6 3 6 6 0 +# +CB 6 0 0 66 3 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +N3 7 0 0 0 4 6 0 0 0 0 + 6 0 0 0 0 + 6 0 0 0 0 +N 7 0 0 0 3 6 4 6 6 1 + 6 4 6 6 1 + 1 1 0 0 0 +# +# cation definitions +# +# +CL 17 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +#OG 8 0 0 0 2 6 4 0 0 0 +# 6 4 0 0 0 +# 0 0 0 0 0 +End +# diff --git a/src/data/amber_u/CTT.frg b/src/data/amber_u/CTT.frg new file mode 100644 index 0000000..9740331 --- /dev/null +++ b/src/data/amber_u/CTT.frg @@ -0,0 +1,14 @@ +# Fragment file for flexible CCl4 +$CCl + 5 1 1 0 +CCl + 1 C CT 0 0 0 1 1 -0.388000 0.000000 + 2CL1 CL 0 0 0 1 1 0.097000 0.000000 + 3CL2 CL 0 0 0 1 1 0.097000 0.000000 + 4CL3 CL 0 0 0 1 1 0.097000 0.000000 + 5CL4 CL 0 0 0 1 1 0.097000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + diff --git a/src/data/amber_u/amber.par b/src/data/amber_u/amber.par new file mode 100644 index 0000000..cab5748 --- /dev/null +++ b/src/data/amber_u/amber.par @@ -0,0 +1,26 @@ +AMBER 99 parameter extensions: SPC/E water, Quantum OH groups, Solvents +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +HWS 1.00800 6.56887E-02 6.00000E-02 1 1111111111 + Q 1 3.28443E-02 6.00000E-02 ERV000001 JACS 117, 5179-5197 (1995) +HO 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + Q 1 4.60240E-02 1.32000E-01 J.Phys.ChemB,109,2005,p15876 +OH 15.99940 6.52704E-01 1.79800E-01 1 1111111111 + Q 8 3.26352E-01 1.79800E-01 J.Phys.ChemB,109,2005,p15876 +OWS 15.99940 7.11280E-01 1.68370E-01 1 1111111111 + Q 8 3.55640E-01 1.68370E-01 ERV000001 +CL 35.45300 0.41840E+00 2.47000E-01 1 1111111111 + 17 0.20920E+00 2.47000E-01 +Bonds +CL -CT 0.17580 1.94472E+05 ERV000003 Fox & Kollman, JPCB 102, 8070-8079 (1998) +CT -H3 0.11000 2.84512E+05 ERV000003 Fox & Kollman, JPCB 102, 8070-8079 (1998) +Angles +H3 -CT -CL 1.87972 3.18821E+02 ERV000003 Fox & Kollman, JPCB 102, 8070-8079 (1998) +CL -CT -CL 1.94255 6.50194E+02 ERV000003 Fox & Kollman, JPCB 102, 8070-8079 (1998) +Proper dihedrals +Improper dihedrals +Atom types +End + diff --git a/src/data/amber_x/amber.par b/src/data/amber_x/amber.par new file mode 100644 index 0000000..c7195ce --- /dev/null +++ b/src/data/amber_x/amber.par @@ -0,0 +1,20 @@ +AMBER 95 parameter extensions: SPC/E water, GLYCAM93, Solvents +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +HWS 1.00800 0.00000E+00 0.00000E+00 1 1111111111 + 1 0.00000E+00 0.00000E+00 TPS000106 Berendsen et al., JPC 91, 6269-6271 (1987) +OWS 15.99940 6.50168E-01 1.77661E-01 1 1111111111 + 8 3.25084E-01 1.77661E-01 TPS000106 Berendsen et al., JPC 91, 6269-6271 (1987) +Cross +Bonds +OWS -HWS 0.10000 0.46275E+06 tps000929 Berendsen et al., JPC 91, 6269-6271 (1987) +HWS -HWS 0.16667 0.46275E+06 tps000929 Berendsen et al., JPC 91, 6269-6271 (1987) +Angles +HWS -OWS -HWS 1.91061 8.36800E+02 +Proper dihedrals +Improper dihedrals +Atom types +End + diff --git a/src/data/amber_x/clfm.sgm b/src/data/amber_x/clfm.sgm new file mode 100644 index 0000000..ba0717b --- /dev/null +++ b/src/data/amber_x/clfm.sgm @@ -0,0 +1,35 @@ +# This is an automatically generated segment file +# + 4.600000 + 5 4 6 0 0 0 1 1 + 0.000000 + 1 C1 0 0 0 1 1 + CT -0.384700 0.000000 + 2 H1 0 0 0 1 1 + H3 0.265900 0.000000 + 3Cl1 0 0 0 1 1 + CL 0.039600 0.000000 + 4Cl2 0 0 0 1 1 + CL 0.039600 0.000000 + 5Cl3 0 0 0 1 1 + CL 0.039600 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 2 1 5 0 0 + 0.000000 0.00000E+00 + 4 3 1 4 0 0 + 0.000000 0.00000E+00 + 5 3 1 5 0 0 + 0.000000 0.00000E+00 + 6 4 1 5 0 0 + 0.000000 0.00000E+00 diff --git a/src/data/amber_x/glycam.par b/src/data/amber_x/glycam.par new file mode 100644 index 0000000..8ddfc20 --- /dev/null +++ b/src/data/amber_x/glycam.par @@ -0,0 +1,188 @@ +AMBER 95 parameter extensions: SPC/E water, GLYCAM93, Solvents +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +HWS 1.00800 0.00000E+00 0.00000E+00 1 1111111111 + 1 0.00000E+00 0.00000E+00 TPS000106 Berendsen et al., JPC 91, 6269-6271 (1987) +OWS 15.99940 6.50168E-01 1.77661E-01 1 1111111111 + 8 3.25084E-01 1.77661E-01 TPS000106 Berendsen et al., JPC 91, 6269-6271 (1987) +AC 12.01000 2.51040E-01 1.80000E-01 1 1111111111 + 6 1.25520E-01 1.80000E-01 TPS000106 Woods et al.,JPC 99, 3832-3846 (1995) +EC 12.01000 2.51040E-01 1.80000E-01 1 1111111111 + 6 1.25520E-01 1.80000E-01 TPS000106 Woods et al.,JPC 99, 3832-3846 (1995) +OG 16.00000 6.27600E-01 1.65000E-01 1 1111111111 + 8 3.13800E-01 1.65000E-01 TPS000106 Woods et al.,JPC 99, 3832-3846 (1995) +Cross +Bonds +OWS -HWS 0.10000 0.46275E+06 tps000929 Berendsen et al., JPC 91, 6269-6271 (1987) +HWS -HWS 0.16667 0.46275E+06 tps000929 Berendsen et al., JPC 91, 6269-6271 (1987) +AC -CT 0.15270 2.59408E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -HC 0.10900 2.76981E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -OS 0.14160 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -OG 0.14050 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -OH 0.13960 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT 0.15190 2.59408E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -HC 0.10900 2.76981E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -N 0.14600 2.82002E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -OS 0.14250 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -OG 0.13890 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -OH 0.13870 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG 0.14350 2.67776E+05 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CL -CT 0.17580 1.94472E+05 erv001018 Fox and Kollman, JPCB 102, 8070-8079 (1998) +CT -H3 0.11000 2.84512E+05 erv001018 Fox and Kollman, JPCB 102, 8070-8079 (1998) +FE -NB 0.20100 5.02080E+04 tps020326 http://pharmacy.man.ac.uk/amber/cof/frcmod.hemall +Angles +AC -CT -CT 1.95128 3.34720E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -HC 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OH 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OG 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OS 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -OG -CT 1.98618 5.02080E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -OH -HO 1.89368 4.60240E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -OS -CT 1.98095 5.02080E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -CT 1.90939 3.34720E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -HC 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -N 1.91463 6.69440E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OH 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OG 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OS 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -OG -CT 2.00189 5.02080E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -OS 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -CT -OG 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -AC -OG 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -AC -OH 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -AC -OS 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -HC 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -N 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -OG 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -OH -HO 1.89368 4.60240E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -OS -CT 1.95302 5.02080E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -N -C 2.12756 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -N -H 2.06647 3.17984E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -AC -HC 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -AC -OG 1.88146 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -AC -OH 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -AC -OS 1.92859 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -HC 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -N 1.91463 6.69440E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -OG 1.89717 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -OH 1.91114 4.18400E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -OH 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -OS 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -CT -OG 1.91114 2.92880E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +N -EC -OS 1.88321 8.94539E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OG -AC -OS 1.95477 9.26338E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -AC -OS 1.94779 9.26338E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OG -EC -OS 1.87797 9.26338E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -EC -OS 1.87099 9.26338E+02 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +H3 -CT -CL 1.87972 3.18821E+02 erv001018 Fox and Kollman, JPCB 102, 8070-8079 (1998) +CL -CT -CL 1.94255 6.50194E+02 erv001018 Fox and Kollman, JPCB 102, 8070-8079 (1998) +CR -NB -FE 1.91986 0.00000E+00 tps020326 http://pharmacy.man.ac.uk/amber/cof/frcmod.hemall +CV -NB -FE 1.91986 0.00000E+00 tps020326 http://pharmacy.man.ac.uk/amber/cof/frcmod.hemall +C -CM -N* 2.04204 5.85760E+02 tps020326 http://pharmacy.man.ac.uk/amber/cof/FADH-.frcfld +CA -CB -N* 2.08043 5.85760E+02 tps020326 http://pharmacy.man.ac.uk/amber/cof/FADH-.frcfld +N* -CM -N* 2.14675 5.85760E+02 tps020326 http://pharmacy.man.ac.uk/amber/cof/FADH-.frcfld +CB -N* -CM 2.00189 5.85760E+02 tps020326 http://pharmacy.man.ac.uk/amber/cof/FADH-.frcfld +Proper dihedrals + -CT -AC - 0.00000 6.04356E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) + -CT -EC - 0.00000 6.04356E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) + -CT -OG - 0.00000 1.60387E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) + -AC -OS - 0.00000 1.60387E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) + -EC -OS - 0.00000 1.60387E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -C -N -EC 3.14159 1.04600E+01 2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -N -C 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -N -C 0.36233 2.59408E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -N -C 0.45483 1.79912E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -N -C 5.92208-7.53120E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -N -C 0.36233 2.59408E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -N -C 0.45483 1.79912E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -N -C 5.92208-7.53120E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -N -C -O 3.14159 1.04600E+01 2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +H -N -EC -HC 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +H -N -EC -CT 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +H -N -EC -OS 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +H -N -CT -AC 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +H -N -CT -EC 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -N -C 0.00000 0.00000E+00 1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -EC -N -C 3.49607 9.99976E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -EC -N -C 6.27149 5.85760E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -EC -N -C 3.05468-1.71544E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -AC -OG -CT 0.00000 0.00000E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -EC -OG -CT 0.00000 0.00000E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG -AC -OS 4.81309 5.81576E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG -AC -OS 5.44613 2.92880E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG -AC -OS 6.06886 3.80744E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG -EC -OS 2.51432 3.55640E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG -EC -OS 6.17061 3.09616E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -OG -EC -OS 0.11222 4.05848E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -AC -OG -CT 0.00000 0.00000E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -OG -CT 0.00000 0.00000E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -CT -OG 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -CT -OG 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -CT -OG -EC 3.14159 8.36800E-01 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -CT -OG -EC 0.00000 1.60247E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OG -AC 3.14159 8.36800E-01 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OG -AC 0.00000 1.60247E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OG -EC 3.14159 8.36800E-01 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OG -EC 0.00000 1.60247E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OG -AC 3.14159 8.36800E-01 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OG -AC 0.00000 1.60247E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OG -EC 3.14159 8.36800E-01 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OG -EC 0.00000 1.60247E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -CT -OS 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -CT -OS 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -CT -OS 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -AC -OS 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -AC -OS 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -AC -OS 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -CT -OS 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -CT -OS 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -CT -OS 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -AC -OG 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -AC -OG 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -AC -OG 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -AC -CT -OH 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -AC -CT -OH 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -AC -CT -OH 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -EC -CT -OH 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -EC -CT -OH 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -EC -CT -OH 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -EC -OG 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -EC -OG 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -EC -OG 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -AC -OG 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -AC -OG 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -AC -OG 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -EC -OG 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -EC -OG 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -CT -EC -OG 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -EC -OS 0.00000 5.60656E+00 -1 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -EC -OS 3.14159-4.81160E+00 -2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OH -CT -EC -OS 0.00000 3.22168E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +AC -CT -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +EC -CT -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -AC -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -AC -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +HC -EC -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -AC -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +OS -EC -OH -HO 0.00000 6.97333E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -CT -OG -AC 0.00000 1.60247E+00 -3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +CT -CT -OG -AC 3.14159 8.36800E-01 2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +# +# The GLYCAM-93 parameter file defines the additional parameters not found in the JPC paper +# These parameters redefine standard AMBER parameters and are, therefore, commented out +# +# -CT -CT - 0.00000 6.04356E-01 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +# -CT -OS - 0.00000 1.60387E+00 3 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +# H -N -C -O 3.14159 1.04600E+01 2 tps000929 Woods et al., JPC 99, 3832-3846 (1995) +# +Improper dihedrals +Atom types +AC 6 0 6 0 4 6 4 6 0 0 + 8 2 6 0 0 + 8 2 6 0 0 +CL 17 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +End diff --git a/src/data/amber_x/meoh.sgm b/src/data/amber_x/meoh.sgm new file mode 100644 index 0000000..7632953 --- /dev/null +++ b/src/data/amber_x/meoh.sgm @@ -0,0 +1,47 @@ +# This is an automatically generated segment file +# + 4.600000 + 6 5 7 3 0 0 1 1 + 0.000000 + 1 C1 0 0 0 1 1 + CT 0.161604 0.000000 + 22H1 0 0 0 1 1 + H1 0.025462 0.000000 + 33H1 0 0 0 1 1 + H1 0.025462 0.000000 + 44H1 0 0 0 1 1 + H1 0.025462 0.000000 + 5 O2 0 0 0 1 1 + OH -0.666187 0.000000 + 62H2 0 0 0 1 1 + HO 0.428197 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 5 0 0 + 0.000000 0.00000E+00 + 5 5 6 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 2 1 5 0 0 + 0.000000 0.00000E+00 + 4 3 1 4 0 0 + 0.000000 0.00000E+00 + 5 3 1 5 0 0 + 0.000000 0.00000E+00 + 6 4 1 5 0 0 + 0.000000 0.00000E+00 + 7 1 5 6 0 0 + 0.000000 0.00000E+00 + 1 2 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 2 3 1 5 6 0 0 + 0 0.000000 0.00000E+00 + 3 4 1 5 6 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/amber_x/spce.sgm b/src/data/amber_x/spce.sgm new file mode 100644 index 0000000..ae37e49 --- /dev/null +++ b/src/data/amber_x/spce.sgm @@ -0,0 +1,17 @@ +# +$spce + 4.600000 + 3 3 0 0 0 0 1 1 + 5.220000 + 1 OW 1 1 0 1 1 + OWS -0.847600 0.000000 + 22HW 0 0 0 1 1 + HWS 0.423800 0.000000 + 33HW 0 0 0 1 1 + HWS 0.423800 0.000000 + 1 1 2 1 1 + 0.100000 0.10000E+07 + 2 1 3 1 1 + 0.100000 0.10000E+07 + 3 2 3 1 1 + 0.163333 0.10000E+07 diff --git a/src/data/amber_x/thfs.sgm b/src/data/amber_x/thfs.sgm new file mode 100644 index 0000000..6ecf71e --- /dev/null +++ b/src/data/amber_x/thfs.sgm @@ -0,0 +1,173 @@ +# This is an automatically generated segment file +# + 4.600000 + 13 13 25 33 0 0 1 1 + 0.000000 + 1 C1 0 0 0 1 1 + CT 0.347397 0.000000 + 22H1 0 0 0 1 1 + H1 -0.036727 0.000000 + 33H1 0 0 0 1 1 + H1 -0.036727 0.000000 + 4 C2 0 0 0 1 1 + CT -0.018154 0.000000 + 52H2 0 0 0 1 1 + HC 0.000963 0.000000 + 63H2 0 0 0 1 1 + HC 0.000963 0.000000 + 7 C3 0 0 0 1 1 + CT -0.018154 0.000000 + 82H3 0 0 0 1 1 + HC 0.000963 0.000000 + 93H3 0 0 0 1 1 + HC 0.000963 0.000000 + 10 C4 0 0 0 1 1 + CT 0.347397 0.000000 + 112H4 0 0 0 1 1 + H1 -0.036727 0.000000 + 123H4 0 0 0 1 1 + H1 -0.036727 0.000000 + 13 O 0 0 0 1 1 + OS -0.515429 0.000000 + 1 1 2 0 0 + 0.000000 0.00000E+00 + 2 1 3 0 0 + 0.000000 0.00000E+00 + 3 1 4 0 0 + 0.000000 0.00000E+00 + 4 1 13 0 0 + 0.000000 0.00000E+00 + 5 4 5 0 0 + 0.000000 0.00000E+00 + 6 4 6 0 0 + 0.000000 0.00000E+00 + 7 4 7 0 0 + 0.000000 0.00000E+00 + 8 7 8 0 0 + 0.000000 0.00000E+00 + 9 7 9 0 0 + 0.000000 0.00000E+00 + 10 7 10 0 0 + 0.000000 0.00000E+00 + 11 10 11 0 0 + 0.000000 0.00000E+00 + 12 10 12 0 0 + 0.000000 0.00000E+00 + 13 10 13 0 0 + 0.000000 0.00000E+00 + 1 2 1 3 0 0 + 0.000000 0.00000E+00 + 2 2 1 4 0 0 + 0.000000 0.00000E+00 + 3 2 1 13 0 0 + 0.000000 0.00000E+00 + 4 3 1 4 0 0 + 0.000000 0.00000E+00 + 5 3 1 13 0 0 + 0.000000 0.00000E+00 + 6 4 1 13 0 0 + 0.000000 0.00000E+00 + 7 1 4 5 0 0 + 0.000000 0.00000E+00 + 8 1 4 6 0 0 + 0.000000 0.00000E+00 + 9 1 4 7 0 0 + 0.000000 0.00000E+00 + 10 5 4 6 0 0 + 0.000000 0.00000E+00 + 11 5 4 7 0 0 + 0.000000 0.00000E+00 + 12 6 4 7 0 0 + 0.000000 0.00000E+00 + 13 4 7 8 0 0 + 0.000000 0.00000E+00 + 14 4 7 9 0 0 + 0.000000 0.00000E+00 + 15 4 7 10 0 0 + 0.000000 0.00000E+00 + 16 8 7 9 0 0 + 0.000000 0.00000E+00 + 17 8 7 10 0 0 + 0.000000 0.00000E+00 + 18 9 7 10 0 0 + 0.000000 0.00000E+00 + 19 7 10 11 0 0 + 0.000000 0.00000E+00 + 20 7 10 12 0 0 + 0.000000 0.00000E+00 + 21 7 10 13 0 0 + 0.000000 0.00000E+00 + 22 11 10 12 0 0 + 0.000000 0.00000E+00 + 23 11 10 13 0 0 + 0.000000 0.00000E+00 + 24 12 10 13 0 0 + 0.000000 0.00000E+00 + 25 1 13 10 0 0 + 0.000000 0.00000E+00 + 1 2 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 2 2 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 3 2 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 4 3 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 5 3 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 6 3 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 7 13 1 4 5 0 0 + 0 0.000000 0.00000E+00 + 8 13 1 4 6 0 0 + 0 0.000000 0.00000E+00 + 9 13 1 4 7 0 0 + 0 0.000000 0.00000E+00 + 10 2 1 13 10 0 0 + 0 0.000000 0.00000E+00 + 11 3 1 13 10 0 0 + 0 0.000000 0.00000E+00 + 12 4 1 13 10 0 0 + 0 0.000000 0.00000E+00 + 13 1 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 14 1 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 15 1 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 16 5 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 17 5 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 18 5 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 19 6 4 7 8 0 0 + 0 0.000000 0.00000E+00 + 20 6 4 7 9 0 0 + 0 0.000000 0.00000E+00 + 21 6 4 7 10 0 0 + 0 0.000000 0.00000E+00 + 22 4 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 23 4 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 24 4 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 25 8 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 26 8 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 27 8 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 28 9 7 10 11 0 0 + 0 0.000000 0.00000E+00 + 29 9 7 10 12 0 0 + 0 0.000000 0.00000E+00 + 30 9 7 10 13 0 0 + 0 0.000000 0.00000E+00 + 31 7 10 13 1 0 0 + 0 0.000000 0.00000E+00 + 32 11 10 13 1 0 0 + 0 0.000000 0.00000E+00 + 33 12 10 13 1 0 0 + 0 0.000000 0.00000E+00 diff --git a/src/data/charmm_s/ALA.frg b/src/data/charmm_s/ALA.frg new file mode 100644 index 0000000..b3ddc7c --- /dev/null +++ b/src/data/charmm_s/ALA.frg @@ -0,0 +1,22 @@ +$ALA + 10 1 1 0 +ALA + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT3 0 0 0 2 1 -0.270000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 84HB HA 0 0 0 2 1 0.090000 0.000000 + 9 C C 2 1 0 3 1 0.510000 0.000000 + 10 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 9 + 5 6 + 5 7 + 5 8 + 9 10 diff --git a/src/data/charmm_s/ALA_C.frg b/src/data/charmm_s/ALA_C.frg new file mode 100644 index 0000000..a5d7b23 --- /dev/null +++ b/src/data/charmm_s/ALA_C.frg @@ -0,0 +1,24 @@ +$ALA_C + 11 1 1 0 +ALA_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT3 0 0 0 2 1 -0.270000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 84HB HA 0 0 0 2 1 0.090000 0.000000 + 9 C CC 0 0 0 3 1 0.340000 0.000000 + 10 O OC 0 0 0 3 1 -0.670000 0.000000 + 11 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 9 + 5 6 + 5 7 + 5 8 + 9 10 + 9 11 diff --git a/src/data/charmm_s/ALA_N.frg b/src/data/charmm_s/ALA_N.frg new file mode 100644 index 0000000..925d0fa --- /dev/null +++ b/src/data/charmm_s/ALA_N.frg @@ -0,0 +1,26 @@ +$ALA_N + 12 1 1 0 +ALA_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT3 0 0 0 2 1 -0.270000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 104HB HA 0 0 0 2 1 0.090000 0.000000 + 11 C C 2 1 0 3 1 0.510000 0.000000 + 12 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 12 diff --git a/src/data/charmm_s/ARG.frg b/src/data/charmm_s/ARG.frg new file mode 100644 index 0000000..af1f1d2 --- /dev/null +++ b/src/data/charmm_s/ARG.frg @@ -0,0 +1,50 @@ +$ARG + 24 1 1 0 +ARG + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CT2 0 0 0 4 1 0.200000 0.000000 + 122HD HA 0 0 0 4 1 0.090000 0.000000 + 133HD HA 0 0 0 4 1 0.090000 0.000000 + 14 NE NC2 0 0 0 4 1 -0.700000 0.000000 + 15 HE HC 0 0 0 4 1 0.440000 0.000000 + 16 CZ C 0 1 0 4 1 0.640000 0.000000 + 17 NH1 NC2 0 0 0 4 1 -0.800000 0.000000 + 182HH1 HC 0 0 0 4 1 0.460000 0.000000 + 193HH1 HC 0 0 0 4 1 0.460000 0.000000 + 20 NH2 NC2 0 0 0 4 1 -0.800000 0.000000 + 212HH2 HC 0 0 0 4 1 0.460000 0.000000 + 223HH2 HC 0 0 0 4 1 0.460000 0.000000 + 23 C C 2 1 0 5 1 0.510000 0.000000 + 24 O O 0 0 0 5 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 23 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 16 17 + 16 20 + 17 18 + 17 19 + 20 21 + 20 22 + 23 24 diff --git a/src/data/charmm_s/ARG_C.frg b/src/data/charmm_s/ARG_C.frg new file mode 100644 index 0000000..13b5c1c --- /dev/null +++ b/src/data/charmm_s/ARG_C.frg @@ -0,0 +1,52 @@ +$ARG_C + 25 1 1 0 +ARG_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CT2 0 0 0 4 1 0.200000 0.000000 + 122HD HA 0 0 0 4 1 0.090000 0.000000 + 133HD HA 0 0 0 4 1 0.090000 0.000000 + 14 NE NC2 0 0 0 4 1 -0.700000 0.000000 + 15 HE HC 0 0 0 4 1 0.440000 0.000000 + 16 CZ C 0 1 0 4 1 0.640000 0.000000 + 17 NH1 NC2 0 0 0 4 1 -0.800000 0.000000 + 182HH1 HC 0 0 0 4 1 0.460000 0.000000 + 193HH1 HC 0 0 0 4 1 0.460000 0.000000 + 20 NH2 NC2 0 0 0 4 1 -0.800000 0.000000 + 212HH2 HC 0 0 0 4 1 0.460000 0.000000 + 223HH2 HC 0 0 0 4 1 0.460000 0.000000 + 23 C CC 0 0 0 3 1 0.340000 0.000000 + 24 O OC 0 0 0 3 1 -0.670000 0.000000 + 25 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 23 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 16 17 + 16 20 + 17 18 + 17 19 + 20 21 + 20 22 + 23 24 + 23 25 diff --git a/src/data/charmm_s/ARG_N.frg b/src/data/charmm_s/ARG_N.frg new file mode 100644 index 0000000..3d2ef7c --- /dev/null +++ b/src/data/charmm_s/ARG_N.frg @@ -0,0 +1,54 @@ +$ARG_N + 26 1 1 0 +ARG_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 CD CT2 0 0 0 4 1 0.200000 0.000000 + 142HD HA 0 0 0 4 1 0.090000 0.000000 + 153HD HA 0 0 0 4 1 0.090000 0.000000 + 16 NE NC2 0 0 0 4 1 -0.700000 0.000000 + 17 HE HC 0 0 0 4 1 0.440000 0.000000 + 18 CZ C 0 1 0 4 1 0.640000 0.000000 + 19 NH1 NC2 0 0 0 4 1 -0.800000 0.000000 + 202HH1 HC 0 0 0 4 1 0.460000 0.000000 + 213HH1 HC 0 0 0 4 1 0.460000 0.000000 + 22 NH2 NC2 0 0 0 4 1 -0.800000 0.000000 + 232HH2 HC 0 0 0 4 1 0.460000 0.000000 + 243HH2 HC 0 0 0 4 1 0.460000 0.000000 + 25 C C 2 1 0 5 1 0.510000 0.000000 + 26 O O 0 0 0 5 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 25 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 + 16 17 + 16 18 + 18 19 + 18 22 + 19 20 + 19 21 + 22 23 + 22 24 + 25 26 diff --git a/src/data/charmm_s/ASN.frg b/src/data/charmm_s/ASN.frg new file mode 100644 index 0000000..9637d35 --- /dev/null +++ b/src/data/charmm_s/ASN.frg @@ -0,0 +1,30 @@ +$ASN + 14 1 1 0 +ASN + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CC 0 1 0 3 1 0.550000 0.000000 + 9 OD1 O 0 0 0 3 1 -0.550000 0.000000 + 10 ND2 NH2 0 1 0 4 1 -0.620000 0.000000 + 112HD2 H 0 0 0 4 1 0.320000 0.000000 + 123HD2 H 0 0 0 4 1 0.300000 0.000000 + 13 C C 2 1 0 5 1 0.510000 0.000000 + 14 O O 0 0 0 5 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 13 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 10 12 + 13 14 diff --git a/src/data/charmm_s/ASN_C.frg b/src/data/charmm_s/ASN_C.frg new file mode 100644 index 0000000..5b0e877 --- /dev/null +++ b/src/data/charmm_s/ASN_C.frg @@ -0,0 +1,32 @@ +$ASN_C + 15 1 1 0 +ASN_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CC 0 1 0 3 1 0.550000 0.000000 + 9 OD1 O 0 0 0 3 1 -0.550000 0.000000 + 10 ND2 NH2 0 1 0 4 1 -0.620000 0.000000 + 112HD2 H 0 0 0 4 1 0.320000 0.000000 + 123HD2 H 0 0 0 4 1 0.300000 0.000000 + 13 C CC 0 0 0 3 1 0.340000 0.000000 + 14 O OC 0 0 0 3 1 -0.670000 0.000000 + 15 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 13 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 10 11 + 10 12 + 13 14 + 13 15 diff --git a/src/data/charmm_s/ASN_N.frg b/src/data/charmm_s/ASN_N.frg new file mode 100644 index 0000000..0911c3a --- /dev/null +++ b/src/data/charmm_s/ASN_N.frg @@ -0,0 +1,34 @@ +$ASN_N + 16 1 1 0 +ASN_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CC 0 1 0 3 1 0.550000 0.000000 + 11 OD1 O 0 0 0 3 1 -0.550000 0.000000 + 12 ND2 NH2 0 1 0 4 1 -0.620000 0.000000 + 132HD2 H 0 0 0 4 1 0.320000 0.000000 + 143HD2 H 0 0 0 4 1 0.300000 0.000000 + 15 C C 2 1 0 5 1 0.510000 0.000000 + 16 O O 0 0 0 5 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 15 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 12 13 + 12 14 + 15 16 diff --git a/src/data/charmm_s/ASP.frg b/src/data/charmm_s/ASP.frg new file mode 100644 index 0000000..82c212d --- /dev/null +++ b/src/data/charmm_s/ASP.frg @@ -0,0 +1,26 @@ +$ASP + 12 1 1 0 +ASP + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.280000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CC 0 0 0 2 1 0.620000 0.000000 + 9 OD1 OC 0 1 0 2 1 -0.760000 0.000000 + 10 OD2 OC 0 0 0 2 1 -0.760000 0.000000 + 11 C C 2 1 0 3 1 0.510000 0.000000 + 12 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 11 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 11 12 diff --git a/src/data/charmm_s/ASP_C.frg b/src/data/charmm_s/ASP_C.frg new file mode 100644 index 0000000..de60971 --- /dev/null +++ b/src/data/charmm_s/ASP_C.frg @@ -0,0 +1,28 @@ +$ASP_C + 13 1 1 0 +ASP_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.280000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CC 0 0 0 2 1 0.620000 0.000000 + 9 OD1 OC 0 1 0 2 1 -0.760000 0.000000 + 10 OD2 OC 0 0 0 2 1 -0.760000 0.000000 + 11 C CC 0 0 0 3 1 0.340000 0.000000 + 12 O OC 0 0 0 3 1 -0.670000 0.000000 + 13 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 11 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 11 12 + 11 13 diff --git a/src/data/charmm_s/ASP_N.frg b/src/data/charmm_s/ASP_N.frg new file mode 100644 index 0000000..fdbe71c --- /dev/null +++ b/src/data/charmm_s/ASP_N.frg @@ -0,0 +1,30 @@ +$ASP_N + 14 1 1 0 +ASP_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.280000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CC 0 0 0 2 1 0.620000 0.000000 + 11 OD1 OC 0 1 0 2 1 -0.760000 0.000000 + 12 OD2 OC 0 0 0 2 1 -0.760000 0.000000 + 13 C C 2 1 0 3 1 0.510000 0.000000 + 14 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 13 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 13 14 diff --git a/src/data/charmm_s/CO.frg b/src/data/charmm_s/CO.frg new file mode 100644 index 0000000..731d469 --- /dev/null +++ b/src/data/charmm_s/CO.frg @@ -0,0 +1,5 @@ +$CO + 2 1 1 0 +CO + 1 C CM 0 0 0 1 1 0.020000 0.000000 + 2 O OM 0 0 0 1 1 -0.020000 0.000000 diff --git a/src/data/charmm_s/CYS.frg b/src/data/charmm_s/CYS.frg new file mode 100644 index 0000000..68c6f48 --- /dev/null +++ b/src/data/charmm_s/CYS.frg @@ -0,0 +1,24 @@ +$CYS + 11 1 1 0 +CYS + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.110000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 SG S 0 0 0 2 1 -0.230000 0.000000 + 9 HG HS 0 0 0 2 1 0.160000 0.000000 + 10 C C 2 1 0 3 1 0.510000 0.000000 + 11 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 10 + 5 6 + 5 7 + 5 8 + 8 9 + 10 11 diff --git a/src/data/charmm_s/CYS_C.frg b/src/data/charmm_s/CYS_C.frg new file mode 100644 index 0000000..1f5b510 --- /dev/null +++ b/src/data/charmm_s/CYS_C.frg @@ -0,0 +1,27 @@ +$CYSH_C + 12 1 1 0 +CYSH_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.110000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 SG S 0 0 0 2 1 -0.230000 0.000000 + 9 HG HS 0 0 0 2 1 0.160000 0.000000 + 10 C CC 0 0 0 3 1 0.340000 0.000000 + 11 O OC 0 0 0 3 1 -0.670000 0.000000 + 12 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 10 + 5 6 + 5 7 + 5 8 + 8 9 + 10 11 + 10 12 + diff --git a/src/data/charmm_s/CYS_N.frg b/src/data/charmm_s/CYS_N.frg new file mode 100644 index 0000000..4f1305f --- /dev/null +++ b/src/data/charmm_s/CYS_N.frg @@ -0,0 +1,28 @@ +$CYSH_N + 13 1 1 0 +CYSH_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.110000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 SG S 0 0 0 2 1 -0.230000 0.000000 + 11 HG HS 0 0 0 2 1 0.160000 0.000000 + 12 C C 2 1 0 3 1 0.510000 0.000000 + 13 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 12 + 7 8 + 7 9 + 7 10 + 10 11 + 12 13 diff --git a/src/data/charmm_s/CYX.frg b/src/data/charmm_s/CYX.frg new file mode 100644 index 0000000..2ce2f66 --- /dev/null +++ b/src/data/charmm_s/CYX.frg @@ -0,0 +1,22 @@ +$CYX + 10 1 1 0 +CYX + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.100000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 SG SM 3 0 0 2 1 -0.080000 0.000000 + 9 C C 2 1 0 3 1 0.510000 0.000000 + 10 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 9 + 5 6 + 5 7 + 5 8 + 9 10 diff --git a/src/data/charmm_s/CYX_C.frg b/src/data/charmm_s/CYX_C.frg new file mode 100644 index 0000000..e8bac7f --- /dev/null +++ b/src/data/charmm_s/CYX_C.frg @@ -0,0 +1,25 @@ +$CYS_C + 11 1 1 0 +CYS_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.100000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 SG S 3 0 0 2 1 -0.080000 0.000000 + 9 C CC 0 0 0 3 1 0.340000 0.000000 + 10 O OC 0 0 0 3 1 -0.670000 0.000000 + 11 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 9 + 5 6 + 5 7 + 5 8 + 9 10 + 9 11 + diff --git a/src/data/charmm_s/CYX_N.frg b/src/data/charmm_s/CYX_N.frg new file mode 100644 index 0000000..ee79551 --- /dev/null +++ b/src/data/charmm_s/CYX_N.frg @@ -0,0 +1,26 @@ +$CYS_N + 12 1 1 0 +CYS_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.100000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 SG S 3 0 0 2 1 -0.080000 0.000000 + 11 C C 2 1 0 3 1 0.510000 0.000000 + 12 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 12 diff --git a/src/data/charmm_s/DUM.frg b/src/data/charmm_s/DUM.frg new file mode 100644 index 0000000..c0f49bc --- /dev/null +++ b/src/data/charmm_s/DUM.frg @@ -0,0 +1,4 @@ +$DUM + 1 1 1 0 +DUM + 1 DUM DUM 0 0 0 1 1 0.000000 0.000000 diff --git a/src/data/charmm_s/GLN.frg b/src/data/charmm_s/GLN.frg new file mode 100644 index 0000000..6b9a050 --- /dev/null +++ b/src/data/charmm_s/GLN.frg @@ -0,0 +1,36 @@ +$GLN + 17 1 1 0 +GLN + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CC 0 1 0 4 1 0.550000 0.000000 + 12 OE1 O 0 0 0 4 1 -0.550000 0.000000 + 13 NE2 NH2 0 1 0 5 1 -0.620000 0.000000 + 142HE2 H 0 0 0 5 1 0.320000 0.000000 + 153HE2 H 0 0 0 5 1 0.300000 0.000000 + 16 C C 2 1 0 6 1 0.510000 0.000000 + 17 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 16 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 13 14 + 13 15 + 16 17 diff --git a/src/data/charmm_s/GLN_C.frg b/src/data/charmm_s/GLN_C.frg new file mode 100644 index 0000000..47a6d81 --- /dev/null +++ b/src/data/charmm_s/GLN_C.frg @@ -0,0 +1,38 @@ +$GLN_C + 19 1 1 0 +GLN_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CC 0 1 0 4 1 0.550000 0.000000 + 12 OE1 O 0 0 0 4 1 -0.550000 0.000000 + 13 NE2 NH2 0 1 0 5 1 -0.620000 0.000000 + 142HE2 H 0 0 0 5 1 0.320000 0.000000 + 153HE2 H 0 0 0 5 1 0.300000 0.000000 + 16 C CC 0 0 0 3 1 0.340000 0.000000 + 17 O OC 0 0 0 3 1 -0.670000 0.000000 + 18 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 16 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 13 14 + 13 15 + 16 17 + 16 18 diff --git a/src/data/charmm_s/GLN_N.frg b/src/data/charmm_s/GLN_N.frg new file mode 100644 index 0000000..43d6720 --- /dev/null +++ b/src/data/charmm_s/GLN_N.frg @@ -0,0 +1,40 @@ +$GLN_N + 19 1 1 0 +GLN_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 CD CC 0 1 0 4 1 0.550000 0.000000 + 14 OE1 O 0 0 0 4 1 -0.550000 0.000000 + 15 NE2 NH2 0 1 0 5 1 -0.620000 0.000000 + 162HE2 H 0 0 0 5 1 0.320000 0.000000 + 173HE2 H 0 0 0 5 1 0.300000 0.000000 + 18 C C 2 1 0 6 1 0.510000 0.000000 + 19 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 18 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 15 16 + 15 17 + 18 19 diff --git a/src/data/charmm_s/GLU.frg b/src/data/charmm_s/GLU.frg new file mode 100644 index 0000000..9184b1f --- /dev/null +++ b/src/data/charmm_s/GLU.frg @@ -0,0 +1,32 @@ +$GLU + 15 1 1 0 +GLU + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.280000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CC 0 0 0 3 1 0.620000 0.000000 + 12 OE1 OC 0 1 0 3 1 -0.760000 0.000000 + 13 OE2 OC 0 0 0 3 1 -0.760000 0.000000 + 14 C C 2 1 0 4 1 0.510000 0.000000 + 15 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 14 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 14 15 diff --git a/src/data/charmm_s/GLU_C.frg b/src/data/charmm_s/GLU_C.frg new file mode 100644 index 0000000..ba6d3c0 --- /dev/null +++ b/src/data/charmm_s/GLU_C.frg @@ -0,0 +1,34 @@ +$GLU_C + 16 1 1 0 +GLU_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.280000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CC 0 0 0 3 1 0.620000 0.000000 + 12 OE1 OC 0 1 0 3 1 -0.760000 0.000000 + 13 OE2 OC 0 0 0 3 1 -0.760000 0.000000 + 14 C CC 0 0 0 3 1 0.340000 0.000000 + 15 O OC 0 0 0 3 1 -0.670000 0.000000 + 16 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 14 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 14 15 + 14 16 diff --git a/src/data/charmm_s/GLU_N.frg b/src/data/charmm_s/GLU_N.frg new file mode 100644 index 0000000..6d8fb0d --- /dev/null +++ b/src/data/charmm_s/GLU_N.frg @@ -0,0 +1,36 @@ +$GLU_N + 17 1 1 0 +GLU_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CT2 0 0 0 3 1 -0.280000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 CD CC 0 0 0 3 1 0.620000 0.000000 + 14 OE1 OC 0 1 0 3 1 -0.760000 0.000000 + 15 OE2 OC 0 0 0 3 1 -0.760000 0.000000 + 16 C C 2 1 0 4 1 0.510000 0.000000 + 17 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 16 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 16 17 diff --git a/src/data/charmm_s/GLY.frg b/src/data/charmm_s/GLY.frg new file mode 100644 index 0000000..f6c2fe0 --- /dev/null +++ b/src/data/charmm_s/GLY.frg @@ -0,0 +1,16 @@ +$GLY + 7 1 1 0 +GLY + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT2 0 0 0 1 1 -0.020000 0.000000 + 42HA HB 0 0 0 1 1 0.090000 0.000000 + 53HA HB 0 0 0 1 1 0.090000 0.000000 + 6 C C 2 1 0 2 1 0.510000 0.000000 + 7 O O 0 0 0 2 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 diff --git a/src/data/charmm_s/GLY_C.frg b/src/data/charmm_s/GLY_C.frg new file mode 100644 index 0000000..3894d85 --- /dev/null +++ b/src/data/charmm_s/GLY_C.frg @@ -0,0 +1,18 @@ +$GLY_C + 8 1 1 0 +GLY_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT2 0 0 0 1 1 -0.020000 0.000000 + 42HA HB 0 0 0 1 1 0.090000 0.000000 + 53HA HB 0 0 0 1 1 0.090000 0.000000 + 6 C CC 0 0 0 3 1 0.340000 0.000000 + 7 O OC 0 0 0 3 1 -0.670000 0.000000 + 8 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 diff --git a/src/data/charmm_s/GLY_N.frg b/src/data/charmm_s/GLY_N.frg new file mode 100644 index 0000000..11b4a33 --- /dev/null +++ b/src/data/charmm_s/GLY_N.frg @@ -0,0 +1,20 @@ +$GLY_N + 9 1 1 0 +GLY_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT2 0 0 0 1 1 0.130000 0.000000 + 62HA HB 0 0 0 1 1 0.090000 0.000000 + 73HA HB 0 0 0 1 1 0.090000 0.000000 + 8 C C 2 1 0 2 1 0.510000 0.000000 + 9 O O 0 0 0 2 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 8 + 8 9 diff --git a/src/data/charmm_s/HEME.frg b/src/data/charmm_s/HEME.frg new file mode 100644 index 0000000..d8ac3c1 --- /dev/null +++ b/src/data/charmm_s/HEME.frg @@ -0,0 +1,156 @@ +$HEME + 73 1 1 0 +HEME + 1FE FE 0 0 0 1 1 0.240000 0.000000 + 2 NA NPH 0 1 0 1 1 -0.180000 0.000000 + 3 NB NPH 0 1 0 1 1 -0.180000 0.000000 + 4 NC NPH 0 1 0 1 1 -0.180000 0.000000 + 5 ND NPH 0 1 0 1 1 -0.180000 0.000000 + 6 C1A CPA 0 1 0 1 1 0.120000 0.000000 + 7 C2A CPB 0 1 0 1 1 -0.060000 0.000000 + 8 C3A CPB 0 1 0 1 1 -0.060000 0.000000 + 9 C4A CPA 0 1 0 1 1 0.120000 0.000000 + 10 C1B CPA 0 1 0 1 1 0.120000 0.000000 + 11 C2B CPB 0 1 0 1 1 -0.060000 0.000000 + 12 C3B CPB 0 1 0 1 1 -0.060000 0.000000 + 13 C4B CPA 0 1 0 1 1 0.120000 0.000000 + 14 C1C CPA 0 1 0 1 1 0.120000 0.000000 + 15 C2C CPB 0 1 0 1 1 -0.060000 0.000000 + 16 C3C CPB 0 1 0 1 1 -0.060000 0.000000 + 17 C4C CPA 0 1 0 1 1 0.120000 0.000000 + 18 C1D CPA 0 1 0 1 1 0.120000 0.000000 + 19 C2D CPB 0 1 0 1 1 -0.060000 0.000000 + 20 C3D CPB 0 1 0 1 1 -0.060000 0.000000 + 21 C4D CPA 0 1 0 1 1 0.120000 0.000000 + 22 CHA CPM 0 1 0 2 1 -0.100000 0.000000 + 23 HA HA 0 0 0 2 1 0.100000 0.000000 + 24 CHB CPM 0 1 0 3 1 -0.100000 0.000000 + 25 HB HA 0 0 0 3 1 0.100000 0.000000 + 26 CHC CPM 0 1 0 4 1 -0.100000 0.000000 + 27 HC HA 0 0 0 4 1 0.100000 0.000000 + 28 CHD CPM 0 1 0 5 1 -0.100000 0.000000 + 29 HD HA 0 0 0 5 1 0.100000 0.000000 + 30 CMA CT3 0 0 0 6 1 -0.270000 0.000000 + 312HMA HA 0 0 0 6 1 0.090000 0.000000 + 323HMA HA 0 0 0 6 1 0.090000 0.000000 + 334HMA HA 0 0 0 6 1 0.090000 0.000000 + 34 CAA CT2 0 0 0 7 1 -0.180000 0.000000 + 352HAA HA 0 0 0 7 1 0.090000 0.000000 + 363HAA HA 0 0 0 7 1 0.090000 0.000000 + 37 CBA CT2 0 0 0 8 1 -0.280000 0.000000 + 382HBA HA 0 0 0 8 1 0.090000 0.000000 + 393HBA HA 0 0 0 8 1 0.090000 0.000000 + 40 CGA CC 0 0 0 8 1 0.620000 0.000000 + 41 O1A OC 0 1 0 8 1 -0.760000 0.000000 + 42 O2A OC 0 0 0 8 1 -0.760000 0.000000 + 43 CMB CT3 0 0 0 9 1 -0.270000 0.000000 + 442HMB HA 0 0 0 9 1 0.090000 0.000000 + 453HMB HA 0 0 0 9 1 0.090000 0.000000 + 464HMB HA 0 0 0 9 1 0.090000 0.000000 + 47 CAB C 0 1 0 10 1 -0.200000 0.000000 + 48 HAB HA 0 1 0 10 1 0.200000 0.000000 + 49 CBB C 0 0 0 11 1 -0.200000 0.000000 + 502HBB HA 0 0 0 11 1 0.100000 0.000000 + 513HBB HA 0 0 0 11 1 0.100000 0.000000 + 52 CMC CT3 0 0 0 12 1 -0.270000 0.000000 + 532HMC HA 0 0 0 12 1 0.090000 0.000000 + 543HMC HA 0 0 0 12 1 0.090000 0.000000 + 554HMC HA 0 0 0 12 1 0.090000 0.000000 + 56 CAC C 0 1 0 13 1 -0.200000 0.000000 + 57 HAC HA 0 1 0 13 1 0.200000 0.000000 + 58 CBC C 0 0 0 14 1 -0.200000 0.000000 + 592HBC HA 0 0 0 14 1 0.100000 0.000000 + 603HBC HA 0 0 0 14 1 0.100000 0.000000 + 61 CMD CT3 0 0 0 15 1 -0.270000 0.000000 + 622HMD HA 0 0 0 15 1 0.090000 0.000000 + 633HMD HA 0 0 0 15 1 0.090000 0.000000 + 644HMD HA 0 0 0 15 1 0.090000 0.000000 + 65 CAD CT2 0 0 0 16 1 -0.180000 0.000000 + 662HAD HA 0 0 0 16 1 0.090000 0.000000 + 673HAD HA 0 0 0 16 1 0.090000 0.000000 + 68 CBD CT2 0 0 0 17 1 -0.280000 0.000000 + 692HBD HA 0 0 0 17 1 0.090000 0.000000 + 703HBD HA 0 0 0 17 1 0.090000 0.000000 + 71 CGD CC 0 0 0 17 1 0.620000 0.000000 + 72 O1D OC 0 1 0 17 1 -0.760000 0.000000 + 73 O2D OC 0 0 0 17 1 -0.760000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 2 6 + 2 9 + 3 10 + 3 13 + 4 14 + 4 17 + 5 18 + 5 21 + 6 7 + 6 22 + 7 8 + 7 34 + 8 9 + 8 30 + 9 24 + 10 11 + 10 24 + 11 12 + 11 43 + 12 13 + 12 47 + 13 26 + 14 15 + 14 26 + 15 16 + 15 52 + 16 17 + 16 56 + 17 28 + 18 19 + 18 28 + 19 20 + 19 61 + 20 21 + 20 65 + 21 22 + 22 23 + 24 25 + 26 27 + 28 29 + 30 31 + 30 32 + 30 33 + 34 35 + 34 36 + 34 37 + 37 38 + 37 39 + 37 40 + 40 41 + 40 42 + 43 44 + 43 45 + 43 46 + 47 48 + 47 49 + 49 50 + 49 51 + 52 53 + 52 54 + 52 55 + 56 57 + 56 58 + 58 59 + 58 60 + 61 62 + 61 63 + 61 64 + 65 66 + 65 67 + 65 68 + 68 69 + 68 70 + 68 71 + 71 72 + 71 73 diff --git a/src/data/charmm_s/HSD.frg b/src/data/charmm_s/HSD.frg new file mode 100644 index 0000000..b6cc382 --- /dev/null +++ b/src/data/charmm_s/HSD.frg @@ -0,0 +1,37 @@ +$HSD + 17 1 1 0 +HSD + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 ND1 NR1 0 1 0 2 1 -0.360000 0.000000 + 6 HD1 H 0 0 0 2 1 0.320000 0.000000 + 7 CG CPH1 0 0 0 2 1 -0.050000 0.000000 + 8 CB CT2 0 0 0 2 1 -0.090000 0.000000 + 92HB HA 0 0 0 2 1 0.090000 0.000000 + 103HB HA 0 0 0 2 1 0.090000 0.000000 + 11 NE2 NR2 0 0 0 3 1 -0.700000 0.000000 + 12 CD2 CPH1 0 1 0 3 1 0.220000 0.000000 + 13 HD2 HR3 0 0 0 3 1 0.100000 0.000000 + 14 CE1 CPH2 0 1 0 3 1 0.250000 0.000000 + 15 HE1 HR1 0 0 0 3 1 0.130000 0.000000 + 16 C C 2 1 0 4 1 0.510000 0.000000 + 17 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 8 + 3 16 + 5 6 + 5 7 + 5 14 + 7 8 + 7 12 + 8 9 + 8 10 + 11 12 + 11 14 + 12 13 + 14 15 + 16 17 diff --git a/src/data/charmm_s/HSD_C.frg b/src/data/charmm_s/HSD_C.frg new file mode 100644 index 0000000..134516f --- /dev/null +++ b/src/data/charmm_s/HSD_C.frg @@ -0,0 +1,39 @@ +$HSD_C + 18 1 1 0 +HSD_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 ND1 NR1 0 1 0 2 1 -0.360000 0.000000 + 6 HD1 H 0 0 0 2 1 0.320000 0.000000 + 7 CG CPH1 0 0 0 2 1 -0.050000 0.000000 + 8 CB CT2 0 0 0 2 1 -0.090000 0.000000 + 92HB HA 0 0 0 2 1 0.090000 0.000000 + 103HB HA 0 0 0 2 1 0.090000 0.000000 + 11 NE2 NR2 0 0 0 3 1 -0.700000 0.000000 + 12 CD2 CPH1 0 1 0 3 1 0.220000 0.000000 + 13 HD2 HR3 0 0 0 3 1 0.100000 0.000000 + 14 CE1 CPH2 0 1 0 3 1 0.250000 0.000000 + 15 HE1 HR1 0 0 0 3 1 0.130000 0.000000 + 16 C CC 0 0 0 3 1 0.340000 0.000000 + 17 O OC 0 0 0 3 1 -0.670000 0.000000 + 18 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 8 + 3 16 + 5 6 + 5 7 + 5 14 + 7 8 + 7 12 + 8 9 + 8 10 + 11 12 + 11 14 + 12 13 + 14 15 + 16 17 + 16 18 diff --git a/src/data/charmm_s/HSD_N.frg b/src/data/charmm_s/HSD_N.frg new file mode 100644 index 0000000..6b9c8de --- /dev/null +++ b/src/data/charmm_s/HSD_N.frg @@ -0,0 +1,41 @@ +$HSD_N + 19 1 1 0 +HSD_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 ND1 NR1 0 1 0 2 1 -0.360000 0.000000 + 8 HD1 H 0 0 0 2 1 0.320000 0.000000 + 9 CG CPH1 0 0 0 2 1 -0.050000 0.000000 + 10 CB CT2 0 0 0 2 1 -0.090000 0.000000 + 112HB HA 0 0 0 2 1 0.090000 0.000000 + 123HB HA 0 0 0 2 1 0.090000 0.000000 + 13 NE2 NR2 0 0 0 3 1 -0.700000 0.000000 + 14 CD2 CPH1 0 1 0 3 1 0.220000 0.000000 + 15 HD2 HR3 0 0 0 3 1 0.100000 0.000000 + 16 CE1 CPH2 0 1 0 3 1 0.250000 0.000000 + 17 HE1 HR1 0 0 0 3 1 0.130000 0.000000 + 18 C C 2 1 0 4 1 0.510000 0.000000 + 19 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 10 + 5 18 + 7 8 + 7 9 + 7 16 + 9 10 + 9 14 + 10 11 + 10 12 + 13 14 + 13 16 + 14 15 + 16 17 + 18 19 diff --git a/src/data/charmm_s/HSE.frg b/src/data/charmm_s/HSE.frg new file mode 100644 index 0000000..006fe31 --- /dev/null +++ b/src/data/charmm_s/HSE.frg @@ -0,0 +1,37 @@ +$HSE + 17 1 1 0 +HSE + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 NE2 NR1 0 1 0 2 1 -0.360000 0.000000 + 6 HE2 H 0 0 0 2 1 0.320000 0.000000 + 7 CD2 CPH1 0 1 0 2 1 -0.050000 0.000000 + 8 HD2 HR3 0 0 0 2 1 0.090000 0.000000 + 9 ND1 NR2 0 0 0 3 1 -0.700000 0.000000 + 10 CG CPH1 0 0 0 3 1 0.220000 0.000000 + 11 CE1 CPH2 0 1 0 3 1 0.250000 0.000000 + 12 HE1 HR1 0 0 0 3 1 0.130000 0.000000 + 13 CB CT2 0 0 0 3 1 -0.080000 0.000000 + 142HB HA 0 0 0 3 1 0.090000 0.000000 + 153HB HA 0 0 0 3 1 0.090000 0.000000 + 16 C C 2 1 0 4 1 0.510000 0.000000 + 17 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 13 + 3 16 + 5 6 + 5 7 + 5 11 + 7 8 + 7 10 + 9 10 + 9 11 + 10 13 + 11 12 + 13 14 + 13 15 + 16 17 diff --git a/src/data/charmm_s/HSE_C.frg b/src/data/charmm_s/HSE_C.frg new file mode 100644 index 0000000..78517b0 --- /dev/null +++ b/src/data/charmm_s/HSE_C.frg @@ -0,0 +1,39 @@ +$HSE_C + 18 1 1 0 +HSE_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 NE2 NR1 0 1 0 2 1 -0.360000 0.000000 + 6 HE2 H 0 0 0 2 1 0.320000 0.000000 + 7 CD2 CPH1 0 1 0 2 1 -0.050000 0.000000 + 8 HD2 HR3 0 0 0 2 1 0.090000 0.000000 + 9 ND1 NR2 0 0 0 3 1 -0.700000 0.000000 + 10 CG CPH1 0 0 0 3 1 0.220000 0.000000 + 11 CE1 CPH2 0 1 0 3 1 0.250000 0.000000 + 12 HE1 HR1 0 0 0 3 1 0.130000 0.000000 + 13 CB CT2 0 0 0 3 1 -0.080000 0.000000 + 142HB HA 0 0 0 3 1 0.090000 0.000000 + 153HB HA 0 0 0 3 1 0.090000 0.000000 + 16 C CC 0 0 0 3 1 0.340000 0.000000 + 17 O OC 0 0 0 3 1 -0.670000 0.000000 + 18 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 13 + 3 16 + 5 6 + 5 7 + 5 11 + 7 8 + 7 10 + 9 10 + 9 11 + 10 13 + 11 12 + 13 14 + 13 15 + 16 17 + 16 18 diff --git a/src/data/charmm_s/HSE_N.frg b/src/data/charmm_s/HSE_N.frg new file mode 100644 index 0000000..90c5251 --- /dev/null +++ b/src/data/charmm_s/HSE_N.frg @@ -0,0 +1,41 @@ +$HSE_N + 19 1 1 0 +HSE_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 NE2 NR1 0 1 0 2 1 -0.360000 0.000000 + 8 HE2 H 0 0 0 2 1 0.320000 0.000000 + 9 CD2 CPH1 0 1 0 2 1 -0.050000 0.000000 + 10 HD2 HR3 0 0 0 2 1 0.090000 0.000000 + 11 ND1 NR2 0 0 0 3 1 -0.700000 0.000000 + 12 CG CPH1 0 0 0 3 1 0.220000 0.000000 + 13 CE1 CPH2 0 1 0 3 1 0.250000 0.000000 + 14 HE1 HR1 0 0 0 3 1 0.130000 0.000000 + 15 CB CT2 0 0 0 3 1 -0.080000 0.000000 + 162HB HA 0 0 0 3 1 0.090000 0.000000 + 173HB HA 0 0 0 3 1 0.090000 0.000000 + 18 C C 2 1 0 4 1 0.510000 0.000000 + 19 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 15 + 5 18 + 7 8 + 7 9 + 7 13 + 9 10 + 9 12 + 11 12 + 11 13 + 12 15 + 13 14 + 15 16 + 15 17 + 18 19 diff --git a/src/data/charmm_s/HSP.frg b/src/data/charmm_s/HSP.frg new file mode 100644 index 0000000..fb29f76 --- /dev/null +++ b/src/data/charmm_s/HSP.frg @@ -0,0 +1,39 @@ +$HSP + 18 1 1 0 +HSP + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 ND1 NR3 0 0 0 2 1 -0.510000 0.000000 + 6 HD1 H 0 1 0 2 1 0.440000 0.000000 + 7 NE2 NR3 0 0 0 2 1 -0.510000 0.000000 + 8 HE2 H 0 1 0 2 1 0.440000 0.000000 + 9 CE1 CPH2 0 0 0 2 1 0.320000 0.000000 + 10 HE1 HR2 0 0 0 2 1 0.180000 0.000000 + 11 CD2 CPH1 0 0 0 3 1 0.190000 0.000000 + 12 HD2 HR1 0 0 0 3 1 0.130000 0.000000 + 13 CG CPH1 0 0 0 3 1 0.190000 0.000000 + 14 CB CT2 0 0 0 3 1 -0.050000 0.000000 + 152HB HA 0 0 0 3 1 0.090000 0.000000 + 163HB HA 0 0 0 3 1 0.090000 0.000000 + 17 C C 2 1 0 4 1 0.510000 0.000000 + 18 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 14 + 3 17 + 5 6 + 5 9 + 5 13 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 17 18 diff --git a/src/data/charmm_s/HSP_C.frg b/src/data/charmm_s/HSP_C.frg new file mode 100644 index 0000000..66551aa --- /dev/null +++ b/src/data/charmm_s/HSP_C.frg @@ -0,0 +1,41 @@ +$HSP_C + 19 1 1 0 +HSP_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 ND1 NR3 0 0 0 2 1 -0.510000 0.000000 + 6 HD1 H 0 1 0 2 1 0.440000 0.000000 + 7 NE2 NR3 0 0 0 2 1 -0.510000 0.000000 + 8 HE2 H 0 1 0 2 1 0.440000 0.000000 + 9 CE1 CPH2 0 0 0 2 1 0.320000 0.000000 + 10 HE1 HR2 0 0 0 2 1 0.180000 0.000000 + 11 CD2 CPH1 0 0 0 3 1 0.190000 0.000000 + 12 HD2 HR1 0 0 0 3 1 0.130000 0.000000 + 13 CG CPH1 0 0 0 3 1 0.190000 0.000000 + 14 CB CT2 0 0 0 3 1 -0.050000 0.000000 + 152HB HA 0 0 0 3 1 0.090000 0.000000 + 163HB HA 0 0 0 3 1 0.090000 0.000000 + 17 C CC 0 0 0 3 1 0.340000 0.000000 + 18 O OC 0 0 0 3 1 -0.670000 0.000000 + 19 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 14 + 3 17 + 5 6 + 5 9 + 5 13 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 13 14 + 14 15 + 14 16 + 17 18 + 17 19 diff --git a/src/data/charmm_s/HSP_N.frg b/src/data/charmm_s/HSP_N.frg new file mode 100644 index 0000000..8de1ca1 --- /dev/null +++ b/src/data/charmm_s/HSP_N.frg @@ -0,0 +1,43 @@ +$HSP_N + 20 1 1 0 +HSP_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 ND1 NR3 0 0 0 2 1 -0.510000 0.000000 + 8 HD1 H 0 1 0 2 1 0.440000 0.000000 + 9 NE2 NR3 0 0 0 2 1 -0.510000 0.000000 + 10 HE2 H 0 1 0 2 1 0.440000 0.000000 + 11 CE1 CPH2 0 0 0 2 1 0.320000 0.000000 + 12 HE1 HR2 0 0 0 2 1 0.180000 0.000000 + 13 CD2 CPH1 0 0 0 3 1 0.190000 0.000000 + 14 HD2 HR1 0 0 0 3 1 0.130000 0.000000 + 15 CG CPH1 0 0 0 3 1 0.190000 0.000000 + 16 CB CT2 0 0 0 3 1 -0.050000 0.000000 + 172HB HA 0 0 0 3 1 0.090000 0.000000 + 183HB HA 0 0 0 3 1 0.090000 0.000000 + 19 C C 2 1 0 4 1 0.510000 0.000000 + 20 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 16 + 5 19 + 7 8 + 7 11 + 7 15 + 9 10 + 9 11 + 9 13 + 11 12 + 12 14 + 12 15 + 15 16 + 16 17 + 16 18 + 19 20 diff --git a/src/data/charmm_s/ILE.frg b/src/data/charmm_s/ILE.frg new file mode 100644 index 0000000..25ee105 --- /dev/null +++ b/src/data/charmm_s/ILE.frg @@ -0,0 +1,40 @@ +$ILE + 19 1 1 0 +ILE + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT1 0 0 0 2 1 -0.090000 0.000000 + 6 HB HA 0 0 0 2 1 0.090000 0.000000 + 7 CG2 CT3 0 0 0 3 1 -0.270000 0.000000 + 82HG2 HA 0 0 0 3 1 0.090000 0.000000 + 93HG2 HA 0 0 0 3 1 0.090000 0.000000 + 104HG2 HA 0 0 0 3 1 0.090000 0.000000 + 11 CG1 CT2 0 0 0 4 1 -0.180000 0.000000 + 122HG1 HA 0 0 0 4 1 0.090000 0.000000 + 133HG1 HA 0 0 0 4 1 0.090000 0.000000 + 14 CD CT3 0 0 0 5 1 -0.270000 0.000000 + 152HD HA 0 0 0 5 1 0.090000 0.000000 + 163HD HA 0 0 0 5 1 0.090000 0.000000 + 174HD HA 0 0 0 5 1 0.090000 0.000000 + 18 C C 2 1 0 6 1 0.510000 0.000000 + 19 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 18 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 14 17 + 18 19 diff --git a/src/data/charmm_s/ILE_C.frg b/src/data/charmm_s/ILE_C.frg new file mode 100644 index 0000000..2ffd521 --- /dev/null +++ b/src/data/charmm_s/ILE_C.frg @@ -0,0 +1,42 @@ +$ILE_C + 20 1 1 0 +ILE_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT1 0 0 0 2 1 -0.090000 0.000000 + 6 HB HA 0 0 0 2 1 0.090000 0.000000 + 7 CG2 CT3 0 0 0 3 1 -0.270000 0.000000 + 82HG2 HA 0 0 0 3 1 0.090000 0.000000 + 93HG2 HA 0 0 0 3 1 0.090000 0.000000 + 104HG2 HA 0 0 0 3 1 0.090000 0.000000 + 11 CG1 CT2 0 0 0 4 1 -0.180000 0.000000 + 122HG1 HA 0 0 0 4 1 0.090000 0.000000 + 133HG1 HA 0 0 0 4 1 0.090000 0.000000 + 14 CD CT3 0 0 0 5 1 -0.270000 0.000000 + 152HD HA 0 0 0 5 1 0.090000 0.000000 + 163HD HA 0 0 0 5 1 0.090000 0.000000 + 174HD HA 0 0 0 5 1 0.090000 0.000000 + 18 C CC 0 0 0 3 1 0.340000 0.000000 + 19 O OC 0 0 0 3 1 -0.670000 0.000000 + 20 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 18 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 14 17 + 18 19 + 18 20 diff --git a/src/data/charmm_s/ILE_N.frg b/src/data/charmm_s/ILE_N.frg new file mode 100644 index 0000000..a4182d9 --- /dev/null +++ b/src/data/charmm_s/ILE_N.frg @@ -0,0 +1,44 @@ +$ILE_N + 21 1 1 0 +ILE_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT1 0 0 0 2 1 -0.090000 0.000000 + 8 HB HA 0 0 0 2 1 0.090000 0.000000 + 9 CG2 CT3 0 0 0 3 1 -0.270000 0.000000 + 102HG2 HA 0 0 0 3 1 0.090000 0.000000 + 113HG2 HA 0 0 0 3 1 0.090000 0.000000 + 124HG2 HA 0 0 0 3 1 0.090000 0.000000 + 13 CG1 CT2 0 0 0 4 1 -0.180000 0.000000 + 142HG1 HA 0 0 0 4 1 0.090000 0.000000 + 153HG1 HA 0 0 0 4 1 0.090000 0.000000 + 16 CD CT3 0 0 0 5 1 -0.270000 0.000000 + 172HD HA 0 0 0 5 1 0.090000 0.000000 + 183HD HA 0 0 0 5 1 0.090000 0.000000 + 194HD HA 0 0 0 5 1 0.090000 0.000000 + 20 C C 2 1 0 6 1 0.510000 0.000000 + 21 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 20 + 7 8 + 7 9 + 7 13 + 9 10 + 9 11 + 9 12 + 13 14 + 13 15 + 13 16 + 16 17 + 16 18 + 16 19 + 20 21 diff --git a/src/data/charmm_s/LEU.frg b/src/data/charmm_s/LEU.frg new file mode 100644 index 0000000..4885446 --- /dev/null +++ b/src/data/charmm_s/LEU.frg @@ -0,0 +1,40 @@ +$LEU + 19 1 1 0 +LEU + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT1 0 0 0 3 1 -0.090000 0.000000 + 9 HG HA 0 0 0 3 1 0.090000 0.000000 + 10 CD1 CT3 0 0 0 4 1 -0.270000 0.000000 + 112HD1 HA 0 0 0 4 1 0.090000 0.000000 + 123HD1 HA 0 0 0 4 1 0.090000 0.000000 + 134HD1 HA 0 0 0 4 1 0.090000 0.000000 + 14 CD2 CT3 0 0 0 5 1 -0.270000 0.000000 + 152HD2 HA 0 0 0 5 1 0.090000 0.000000 + 163HD2 HA 0 0 0 5 1 0.090000 0.000000 + 174HD2 HA 0 0 0 5 1 0.090000 0.000000 + 18 C C 2 1 0 6 1 0.510000 0.000000 + 19 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 18 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 14 + 10 11 + 10 12 + 10 13 + 14 15 + 14 16 + 14 17 + 18 19 diff --git a/src/data/charmm_s/LEU_C.frg b/src/data/charmm_s/LEU_C.frg new file mode 100644 index 0000000..0bac128 --- /dev/null +++ b/src/data/charmm_s/LEU_C.frg @@ -0,0 +1,42 @@ +$LEU_C + 20 1 1 0 +LEU_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT1 0 0 0 3 1 -0.090000 0.000000 + 9 HG HA 0 0 0 3 1 0.090000 0.000000 + 10 CD1 CT3 0 0 0 4 1 -0.270000 0.000000 + 112HD1 HA 0 0 0 4 1 0.090000 0.000000 + 123HD1 HA 0 0 0 4 1 0.090000 0.000000 + 134HD1 HA 0 0 0 4 1 0.090000 0.000000 + 14 CD2 CT3 0 0 0 5 1 -0.270000 0.000000 + 152HD2 HA 0 0 0 5 1 0.090000 0.000000 + 163HD2 HA 0 0 0 5 1 0.090000 0.000000 + 174HD2 HA 0 0 0 5 1 0.090000 0.000000 + 18 C CC 0 0 0 3 1 0.340000 0.000000 + 19 O OC 0 0 0 3 1 -0.670000 0.000000 + 20 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 18 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 14 + 10 11 + 10 12 + 10 13 + 14 15 + 14 16 + 14 17 + 18 19 + 18 20 diff --git a/src/data/charmm_s/LEU_N.frg b/src/data/charmm_s/LEU_N.frg new file mode 100644 index 0000000..278fa9b --- /dev/null +++ b/src/data/charmm_s/LEU_N.frg @@ -0,0 +1,44 @@ +$LEU_N + 21 1 1 0 +LEU_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CT1 0 0 0 3 1 -0.090000 0.000000 + 11 HG HA 0 0 0 3 1 0.090000 0.000000 + 12 CD1 CT3 0 0 0 4 1 -0.270000 0.000000 + 132HD1 HA 0 0 0 4 1 0.090000 0.000000 + 143HD1 HA 0 0 0 4 1 0.090000 0.000000 + 154HD1 HA 0 0 0 4 1 0.090000 0.000000 + 16 CD2 CT3 0 0 0 5 1 -0.270000 0.000000 + 172HD2 HA 0 0 0 5 1 0.090000 0.000000 + 183HD2 HA 0 0 0 5 1 0.090000 0.000000 + 194HD2 HA 0 0 0 5 1 0.090000 0.000000 + 20 C C 2 1 0 6 1 0.510000 0.000000 + 21 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 20 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 16 + 12 13 + 12 14 + 12 15 + 16 17 + 16 18 + 16 19 + 20 21 diff --git a/src/data/charmm_s/LYS.frg b/src/data/charmm_s/LYS.frg new file mode 100644 index 0000000..5c72f1c --- /dev/null +++ b/src/data/charmm_s/LYS.frg @@ -0,0 +1,46 @@ +$LYS + 22 1 1 0 +LYS + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CT2 0 0 0 4 1 -0.180000 0.000000 + 122HD HA 0 0 0 4 1 0.090000 0.000000 + 133HD HA 0 0 0 4 1 0.090000 0.000000 + 14 CE CT2 0 0 0 5 1 0.210000 0.000000 + 152HE HA 0 0 0 5 1 0.050000 0.000000 + 163HE HA 0 0 0 5 1 0.050000 0.000000 + 17 NZ NH3 0 0 0 5 1 -0.300000 0.000000 + 182HZ HC 0 0 0 5 1 0.330000 0.000000 + 193HZ HC 0 0 0 5 1 0.330000 0.000000 + 204HZ HC 0 0 0 5 1 0.330000 0.000000 + 21 C C 2 1 0 6 1 0.510000 0.000000 + 22 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 21 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 + 21 22 diff --git a/src/data/charmm_s/LYS_C.frg b/src/data/charmm_s/LYS_C.frg new file mode 100644 index 0000000..6ae8755 --- /dev/null +++ b/src/data/charmm_s/LYS_C.frg @@ -0,0 +1,48 @@ +$LYS_C + 23 1 1 0 +LYS_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 CD CT2 0 0 0 4 1 -0.180000 0.000000 + 122HD HA 0 0 0 4 1 0.090000 0.000000 + 133HD HA 0 0 0 4 1 0.090000 0.000000 + 14 CE CT2 0 0 0 5 1 0.210000 0.000000 + 152HE HA 0 0 0 5 1 0.050000 0.000000 + 163HE HA 0 0 0 5 1 0.050000 0.000000 + 17 NZ NH3 0 0 0 5 1 -0.300000 0.000000 + 182HZ HC 0 0 0 5 1 0.330000 0.000000 + 193HZ HC 0 0 0 5 1 0.330000 0.000000 + 204HZ HC 0 0 0 5 1 0.330000 0.000000 + 21 C CC 0 0 0 3 1 0.340000 0.000000 + 22 O OC 0 0 0 3 1 -0.670000 0.000000 + 23 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 21 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 + 21 22 + 21 23 diff --git a/src/data/charmm_s/LYS_N.frg b/src/data/charmm_s/LYS_N.frg new file mode 100644 index 0000000..26d10a1 --- /dev/null +++ b/src/data/charmm_s/LYS_N.frg @@ -0,0 +1,50 @@ +$LYS_N + 24 1 1 0 +LYS_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CT2 0 0 0 3 1 -0.180000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 CD CT2 0 0 0 4 1 -0.180000 0.000000 + 142HD HA 0 0 0 4 1 0.090000 0.000000 + 153HD HA 0 0 0 4 1 0.090000 0.000000 + 16 CE CT2 0 0 0 5 1 0.210000 0.000000 + 172HE HA 0 0 0 5 1 0.050000 0.000000 + 183HE HA 0 0 0 5 1 0.050000 0.000000 + 19 NZ NH3 0 0 0 5 1 -0.300000 0.000000 + 202HZ HC 0 0 0 5 1 0.330000 0.000000 + 213HZ HC 0 0 0 5 1 0.330000 0.000000 + 224HZ HC 0 0 0 5 1 0.330000 0.000000 + 23 C C 2 1 0 6 1 0.510000 0.000000 + 24 O O 0 0 0 6 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 23 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 + 16 17 + 16 18 + 16 19 + 19 20 + 19 21 + 19 22 + 23 24 diff --git a/src/data/charmm_s/MET.frg b/src/data/charmm_s/MET.frg new file mode 100644 index 0000000..31490fe --- /dev/null +++ b/src/data/charmm_s/MET.frg @@ -0,0 +1,36 @@ +$MET + 17 1 1 0 +MET + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.140000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 SD S 0 0 0 3 1 -0.090000 0.000000 + 12 CE CT3 0 0 0 3 1 -0.220000 0.000000 + 132HE HA 0 0 0 3 1 0.090000 0.000000 + 143HE HA 0 0 0 3 1 0.090000 0.000000 + 154HE HA 0 0 0 3 1 0.090000 0.000000 + 16 C C 2 1 0 4 1 0.510000 0.000000 + 17 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 16 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 12 13 + 12 14 + 12 15 + 16 17 diff --git a/src/data/charmm_s/MET_C.frg b/src/data/charmm_s/MET_C.frg new file mode 100644 index 0000000..4d9e876 --- /dev/null +++ b/src/data/charmm_s/MET_C.frg @@ -0,0 +1,38 @@ +$MET_C + 18 1 1 0 +MET_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CT2 0 0 0 3 1 -0.140000 0.000000 + 92HG HA 0 0 0 3 1 0.090000 0.000000 + 103HG HA 0 0 0 3 1 0.090000 0.000000 + 11 SD S 0 0 0 3 1 -0.090000 0.000000 + 12 CE CT3 0 0 0 3 1 -0.220000 0.000000 + 132HE HA 0 0 0 3 1 0.090000 0.000000 + 143HE HA 0 0 0 3 1 0.090000 0.000000 + 154HE HA 0 0 0 3 1 0.090000 0.000000 + 16 C CC 0 0 0 3 1 0.340000 0.000000 + 17 O OC 0 0 0 3 1 -0.670000 0.000000 + 18 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 16 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 12 13 + 12 14 + 12 15 + 16 17 + 16 18 diff --git a/src/data/charmm_s/MET_N.frg b/src/data/charmm_s/MET_N.frg new file mode 100644 index 0000000..dbf00d4 --- /dev/null +++ b/src/data/charmm_s/MET_N.frg @@ -0,0 +1,40 @@ +$MET_N + 19 1 1 0 +MET_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CT2 0 0 0 3 1 -0.140000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 SD S 0 0 0 3 1 -0.090000 0.000000 + 14 CE CT3 0 0 0 3 1 -0.220000 0.000000 + 152HE HA 0 0 0 3 1 0.090000 0.000000 + 163HE HA 0 0 0 3 1 0.090000 0.000000 + 174HE HA 0 0 0 3 1 0.090000 0.000000 + 18 C C 2 1 0 4 1 0.510000 0.000000 + 19 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 18 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 14 15 + 14 16 + 14 17 + 18 19 diff --git a/src/data/charmm_s/O2.frg b/src/data/charmm_s/O2.frg new file mode 100644 index 0000000..9671fbe --- /dev/null +++ b/src/data/charmm_s/O2.frg @@ -0,0 +1,6 @@ +$O2 + 2 1 1 0 +O2 + 1 O1 OM 0 0 0 1 1 0.020000 0.000000 + 2 O2 OM 0 0 0 1 1 -0.020000 0.000000 + 1 2 diff --git a/src/data/charmm_s/PHE.frg b/src/data/charmm_s/PHE.frg new file mode 100644 index 0000000..aa932ff --- /dev/null +++ b/src/data/charmm_s/PHE.frg @@ -0,0 +1,43 @@ +$PHE + 20 1 1 0 +PHE + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CA 0 0 0 3 1 0.000000 0.000000 + 9 CD1 CA 0 0 0 4 1 -0.115000 0.000000 + 10 HD1 HP 0 0 0 4 1 0.115000 0.000000 + 11 CD2 CA 0 0 0 5 1 -0.115000 0.000000 + 12 HD2 HP 0 0 0 5 1 0.115000 0.000000 + 13 CE1 CA 0 0 0 6 1 -0.115000 0.000000 + 14 HE1 HP 0 0 0 6 1 0.115000 0.000000 + 15 CE2 CA 0 0 0 7 1 -0.115000 0.000000 + 16 HE2 HP 0 0 0 7 1 0.115000 0.000000 + 17 CZ CA 0 0 0 8 1 -0.115000 0.000000 + 18 HZ HP 0 0 0 8 1 0.115000 0.000000 + 19 C C 2 1 0 9 1 0.510000 0.000000 + 20 O O 0 0 0 9 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 19 + 5 6 + 5 7 + 5 8 + 8 9 + 8 11 + 9 10 + 9 13 + 11 12 + 11 15 + 13 14 + 13 17 + 15 16 + 15 17 + 17 18 + 19 20 diff --git a/src/data/charmm_s/PHE_C.frg b/src/data/charmm_s/PHE_C.frg new file mode 100644 index 0000000..2e1591e --- /dev/null +++ b/src/data/charmm_s/PHE_C.frg @@ -0,0 +1,45 @@ +$PHE_C + 21 1 1 0 +PHE_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CA 0 0 0 3 1 0.000000 0.000000 + 9 CD1 CA 0 0 0 4 1 -0.115000 0.000000 + 10 HD1 HP 0 0 0 4 1 0.115000 0.000000 + 11 CD2 CA 0 0 0 5 1 -0.115000 0.000000 + 12 HD2 HP 0 0 0 5 1 0.115000 0.000000 + 13 CE1 CA 0 0 0 6 1 -0.115000 0.000000 + 14 HE1 HP 0 0 0 6 1 0.115000 0.000000 + 15 CE2 CA 0 0 0 7 1 -0.115000 0.000000 + 16 HE2 HP 0 0 0 7 1 0.115000 0.000000 + 17 CZ CA 0 0 0 8 1 -0.115000 0.000000 + 18 HZ HP 0 0 0 8 1 0.115000 0.000000 + 19 C CC 0 0 0 3 1 0.340000 0.000000 + 20 O OC 0 0 0 3 1 -0.670000 0.000000 + 21 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 19 + 5 6 + 5 7 + 5 8 + 8 9 + 8 11 + 9 10 + 9 13 + 11 12 + 11 15 + 13 14 + 13 17 + 15 16 + 15 17 + 17 18 + 19 20 + 19 21 diff --git a/src/data/charmm_s/PHE_N.frg b/src/data/charmm_s/PHE_N.frg new file mode 100644 index 0000000..d61899e --- /dev/null +++ b/src/data/charmm_s/PHE_N.frg @@ -0,0 +1,47 @@ +$PHE_N + 22 1 1 0 +PHE_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CA 0 0 0 3 1 0.000000 0.000000 + 11 CD1 CA 0 0 0 4 1 -0.115000 0.000000 + 12 HD1 HP 0 0 0 4 1 0.115000 0.000000 + 13 CD2 CA 0 0 0 5 1 -0.115000 0.000000 + 14 HD2 HP 0 0 0 5 1 0.115000 0.000000 + 15 CE1 CA 0 0 0 6 1 -0.115000 0.000000 + 16 HE1 HP 0 0 0 6 1 0.115000 0.000000 + 17 CE2 CA 0 0 0 7 1 -0.115000 0.000000 + 18 HE2 HP 0 0 0 7 1 0.115000 0.000000 + 19 CZ CA 0 0 0 8 1 -0.115000 0.000000 + 20 HZ HP 0 0 0 8 1 0.115000 0.000000 + 21 C C 2 1 0 9 1 0.510000 0.000000 + 22 O O 0 0 0 9 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 21 + 7 8 + 7 9 + 7 10 + 10 11 + 10 13 + 11 12 + 11 15 + 13 14 + 13 17 + 15 16 + 15 19 + 17 18 + 17 19 + 19 20 + 21 22 diff --git a/src/data/charmm_s/PRO.frg b/src/data/charmm_s/PRO.frg new file mode 100644 index 0000000..5430522 --- /dev/null +++ b/src/data/charmm_s/PRO.frg @@ -0,0 +1,31 @@ +$PRO + 14 1 1 0 +PRO + 1 N N 1 1 0 1 1 -0.290000 0.000000 + 2 CA CP1 0 0 0 1 1 0.020000 0.000000 + 3 HA HB 0 0 0 1 1 0.090000 0.000000 + 4 CD CP3 0 0 0 1 1 0.000000 0.000000 + 52HD HA 0 0 0 1 1 0.090000 0.000000 + 63HD HA 0 0 0 1 1 0.090000 0.000000 + 7 CB CP2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CP2 0 0 0 3 1 -0.180000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 C C 2 1 0 4 1 0.510000 0.000000 + 14 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 4 + 2 3 + 2 7 + 2 13 + 4 5 + 4 6 + 4 10 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 13 14 diff --git a/src/data/charmm_s/PRO_C.frg b/src/data/charmm_s/PRO_C.frg new file mode 100644 index 0000000..ea0cc19 --- /dev/null +++ b/src/data/charmm_s/PRO_C.frg @@ -0,0 +1,33 @@ +$PRO_C + 15 1 1 0 +PRO_C + 1 N N 1 1 0 1 1 -0.290000 0.000000 + 2 CA CP1 0 0 0 1 1 0.020000 0.000000 + 3 HA HB 0 0 0 1 1 0.090000 0.000000 + 4 CD CP3 0 0 0 1 1 0.000000 0.000000 + 52HD HA 0 0 0 1 1 0.090000 0.000000 + 63HD HA 0 0 0 1 1 0.090000 0.000000 + 7 CB CP2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CP2 0 0 0 3 1 -0.180000 0.000000 + 112HG HA 0 0 0 3 1 0.090000 0.000000 + 123HG HA 0 0 0 3 1 0.090000 0.000000 + 13 C CC 0 0 0 3 1 0.340000 0.000000 + 14 O OC 0 0 0 3 1 -0.670000 0.000000 + 15 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 4 + 2 3 + 2 7 + 2 13 + 4 5 + 4 6 + 4 10 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 13 14 + 13 15 diff --git a/src/data/charmm_s/PRO_N.frg b/src/data/charmm_s/PRO_N.frg new file mode 100644 index 0000000..801ca49 --- /dev/null +++ b/src/data/charmm_s/PRO_N.frg @@ -0,0 +1,35 @@ +$PRO_N + 16 1 1 0 +PRO_N + 1 N N 0 0 0 1 1 -0.070000 0.000000 + 22HN HC 0 0 0 1 1 0.240000 0.000000 + 33HN HC 0 0 0 1 1 0.240000 0.000000 + 4 CA CP1 0 0 0 1 1 0.160000 0.000000 + 5 HA HB 0 0 0 1 1 0.090000 0.000000 + 6 CD CP3 0 0 0 1 1 0.160000 0.000000 + 72HD HA 0 0 0 1 1 0.090000 0.000000 + 83HD HA 0 0 0 1 1 0.090000 0.000000 + 9 CB CP2 0 0 0 2 1 -0.180000 0.000000 + 102HB HA 0 0 0 2 1 0.090000 0.000000 + 113HB HA 0 0 0 2 1 0.090000 0.000000 + 12 CG CP2 0 0 0 3 1 -0.180000 0.000000 + 132HG HA 0 0 0 3 1 0.090000 0.000000 + 143HG HA 0 0 0 3 1 0.090000 0.000000 + 15 C C 2 1 0 4 1 0.510000 0.000000 + 16 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 6 + 4 5 + 4 9 + 4 15 + 6 7 + 6 8 + 6 12 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 15 16 diff --git a/src/data/charmm_s/SER.frg b/src/data/charmm_s/SER.frg new file mode 100644 index 0000000..5465f01 --- /dev/null +++ b/src/data/charmm_s/SER.frg @@ -0,0 +1,24 @@ +$SER + 11 1 1 0 +SER + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 0.050000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 OG OH1 0 0 0 2 1 -0.660000 0.000000 + 9 HG H 0 0 0 2 1 0.430000 0.000000 + 10 C C 2 1 0 3 1 0.510000 0.000000 + 11 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 10 + 5 6 + 5 7 + 5 8 + 8 9 + 10 11 diff --git a/src/data/charmm_s/SER_C.frg b/src/data/charmm_s/SER_C.frg new file mode 100644 index 0000000..2366c4d --- /dev/null +++ b/src/data/charmm_s/SER_C.frg @@ -0,0 +1,26 @@ +$SER_C + 12 1 1 0 +SER_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 0.050000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 OG OH1 0 0 0 2 1 -0.660000 0.000000 + 9 HG H 0 0 0 2 1 0.430000 0.000000 + 10 C CC 0 0 0 3 1 0.340000 0.000000 + 11 O OC 0 0 0 3 1 -0.670000 0.000000 + 12 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 10 + 5 6 + 5 7 + 5 8 + 8 9 + 10 11 + 10 12 diff --git a/src/data/charmm_s/SER_N.frg b/src/data/charmm_s/SER_N.frg new file mode 100644 index 0000000..2ec3ba4 --- /dev/null +++ b/src/data/charmm_s/SER_N.frg @@ -0,0 +1,28 @@ +$SER_N + 13 1 1 0 +SER_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 0.050000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 OG OH1 0 0 0 2 1 -0.660000 0.000000 + 11 HG H 0 0 0 2 1 0.430000 0.000000 + 12 C C 2 1 0 3 1 0.510000 0.000000 + 13 O O 0 0 0 3 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 12 + 7 8 + 7 9 + 7 10 + 10 11 + 12 13 diff --git a/src/data/charmm_s/THR.frg b/src/data/charmm_s/THR.frg new file mode 100644 index 0000000..a9e4297 --- /dev/null +++ b/src/data/charmm_s/THR.frg @@ -0,0 +1,30 @@ +$THR + 14 1 1 0 +THR + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT1 0 0 0 2 1 0.140000 0.000000 + 6 HB HA 0 0 0 2 1 0.090000 0.000000 + 7 OG1 OH1 0 0 0 2 1 -0.660000 0.000000 + 8 HG1 H 0 0 0 2 1 0.430000 0.000000 + 9 CG2 CT3 0 0 0 3 1 -0.270000 0.000000 + 102HG2 HA 0 0 0 3 1 0.090000 0.000000 + 113HG2 HA 0 0 0 3 1 0.090000 0.000000 + 124HG2 HA 0 0 0 3 1 0.090000 0.000000 + 13 C C 2 1 0 4 1 0.510000 0.000000 + 14 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 13 + 5 6 + 5 7 + 5 9 + 7 8 + 9 10 + 9 11 + 9 12 + 13 14 diff --git a/src/data/charmm_s/THR_C.frg b/src/data/charmm_s/THR_C.frg new file mode 100644 index 0000000..eec8de2 --- /dev/null +++ b/src/data/charmm_s/THR_C.frg @@ -0,0 +1,32 @@ +$THR_C + 15 1 1 0 +THR_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT1 0 0 0 2 1 0.140000 0.000000 + 6 HB HA 0 0 0 2 1 0.090000 0.000000 + 7 OG1 OH1 0 0 0 2 1 -0.660000 0.000000 + 8 HG1 H 0 0 0 2 1 0.430000 0.000000 + 9 CG2 CT3 0 0 0 3 1 -0.270000 0.000000 + 102HG2 HA 0 0 0 3 1 0.090000 0.000000 + 113HG2 HA 0 0 0 3 1 0.090000 0.000000 + 124HG2 HA 0 0 0 3 1 0.090000 0.000000 + 13 C CC 0 0 0 3 1 0.340000 0.000000 + 14 O OC 0 0 0 3 1 -0.670000 0.000000 + 15 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 13 + 5 6 + 5 7 + 5 9 + 7 8 + 9 10 + 9 11 + 9 12 + 13 14 + 13 15 diff --git a/src/data/charmm_s/THR_N.frg b/src/data/charmm_s/THR_N.frg new file mode 100644 index 0000000..9941435 --- /dev/null +++ b/src/data/charmm_s/THR_N.frg @@ -0,0 +1,34 @@ +$THR_N + 16 1 1 0 +THR_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT1 0 0 0 2 1 0.140000 0.000000 + 8 HB HA 0 0 0 2 1 0.090000 0.000000 + 9 OG1 OH1 0 0 0 2 1 -0.660000 0.000000 + 10 HG1 H 0 0 0 2 1 0.430000 0.000000 + 11 CG2 CT3 0 0 0 3 1 -0.270000 0.000000 + 122HG2 HA 0 0 0 3 1 0.090000 0.000000 + 133HG2 HA 0 0 0 3 1 0.090000 0.000000 + 144HG2 HA 0 0 0 3 1 0.090000 0.000000 + 15 C C 2 1 0 4 1 0.510000 0.000000 + 16 O O 0 0 0 4 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 15 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 14 + 15 16 diff --git a/src/data/charmm_s/TIP3.frg b/src/data/charmm_s/TIP3.frg new file mode 100644 index 0000000..8bded83 --- /dev/null +++ b/src/data/charmm_s/TIP3.frg @@ -0,0 +1,9 @@ +$TIP3 + 3 1 1 0 +TIP3 + 1 OH2 OT 0 0 0 1 1 -0.830000 0.000000 + 2 H1 HT 0 0 0 1 1 0.410000 0.000000 + 3 H2 HT 0 0 0 1 1 0.410000 0.000000 + 1 2 + 1 3 + 2 3 diff --git a/src/data/charmm_s/TP3M.frg b/src/data/charmm_s/TP3M.frg new file mode 100644 index 0000000..9bba026 --- /dev/null +++ b/src/data/charmm_s/TP3M.frg @@ -0,0 +1,8 @@ +$TP3M + 3 1 1 0 +TP3M + 1 OH2 OT 0 0 0 1 1 -0.830000 0.000000 + 2 H1 HT 0 0 0 1 1 0.410000 0.000000 + 3 H2 HT 0 0 0 1 1 0.410000 0.000000 + 1 2 + 1 3 diff --git a/src/data/charmm_s/TRP.frg b/src/data/charmm_s/TRP.frg new file mode 100644 index 0000000..7882866 --- /dev/null +++ b/src/data/charmm_s/TRP.frg @@ -0,0 +1,52 @@ +$TRP + 24 1 1 0 +TRP + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CY 0 0 0 3 1 -0.030000 0.000000 + 9 CD2 CPT 0 0 0 3 1 -0.020000 0.000000 + 10 CD1 CA 0 0 0 3 1 0.035000 0.000000 + 11 HD1 HP 0 0 0 3 1 0.115000 0.000000 + 12 NE1 NY 0 0 0 3 1 -0.610000 0.000000 + 13 HE1 H 0 0 0 3 1 0.380000 0.000000 + 14 CE2 CPT 0 0 0 3 1 0.130000 0.000000 + 15 CE3 CA 0 0 0 4 1 -0.115000 0.000000 + 16 HE3 HP 0 0 0 4 1 0.115000 0.000000 + 17 CZ2 CA 0 0 0 5 1 -0.115000 0.000000 + 18 HZ2 HP 0 0 0 5 1 0.115000 0.000000 + 19 CZ3 CA 0 0 0 6 1 -0.115000 0.000000 + 20 HZ3 HP 0 0 0 6 1 0.115000 0.000000 + 21 CH2 CA 0 0 0 7 1 -0.115000 0.000000 + 22 HH2 HP 0 0 0 7 1 0.115000 0.000000 + 23 C C 2 1 0 8 1 0.510000 0.000000 + 24 O O 0 0 0 8 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 23 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 9 14 + 9 15 + 10 11 + 10 12 + 12 13 + 12 14 + 14 17 + 15 16 + 15 19 + 17 18 + 17 21 + 19 20 + 19 21 + 21 22 + 23 24 diff --git a/src/data/charmm_s/TRP_C.frg b/src/data/charmm_s/TRP_C.frg new file mode 100644 index 0000000..5dd057b --- /dev/null +++ b/src/data/charmm_s/TRP_C.frg @@ -0,0 +1,54 @@ +$TRP_C + 25 1 1 0 +TRP_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CY 0 0 0 3 1 -0.030000 0.000000 + 9 CD2 CPT 0 0 0 3 1 -0.020000 0.000000 + 10 CD1 CA 0 0 0 3 1 0.035000 0.000000 + 11 HD1 HP 0 0 0 3 1 0.115000 0.000000 + 12 NE1 NY 0 0 0 3 1 -0.610000 0.000000 + 13 HE1 H 0 0 0 3 1 0.380000 0.000000 + 14 CE2 CPT 0 0 0 3 1 0.130000 0.000000 + 15 CE3 CA 0 0 0 4 1 -0.115000 0.000000 + 16 HE3 HP 0 0 0 4 1 0.115000 0.000000 + 17 CZ2 CA 0 0 0 5 1 -0.115000 0.000000 + 18 HZ2 HP 0 0 0 5 1 0.115000 0.000000 + 19 CZ3 CA 0 0 0 6 1 -0.115000 0.000000 + 20 HZ3 HP 0 0 0 6 1 0.115000 0.000000 + 21 CH2 CA 0 0 0 7 1 -0.115000 0.000000 + 22 HH2 HP 0 0 0 7 1 0.115000 0.000000 + 23 C CC 0 0 0 3 1 0.340000 0.000000 + 24 O OC 0 0 0 3 1 -0.670000 0.000000 + 25 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 23 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 9 14 + 9 15 + 10 11 + 10 12 + 12 13 + 12 14 + 14 17 + 15 16 + 15 19 + 17 18 + 17 21 + 19 20 + 19 21 + 21 22 + 23 24 + 23 25 diff --git a/src/data/charmm_s/TRP_N.frg b/src/data/charmm_s/TRP_N.frg new file mode 100644 index 0000000..1f49de7 --- /dev/null +++ b/src/data/charmm_s/TRP_N.frg @@ -0,0 +1,56 @@ +$TRP_N + 26 1 1 0 +TRP_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CY 0 0 0 3 1 -0.030000 0.000000 + 11 CD2 CPT 0 0 0 3 1 -0.020000 0.000000 + 12 CD1 CA 0 0 0 3 1 0.035000 0.000000 + 13 HD1 HP 0 0 0 3 1 0.115000 0.000000 + 14 NE1 NY 0 0 0 3 1 -0.610000 0.000000 + 15 HE1 H 0 0 0 3 1 0.380000 0.000000 + 16 CE2 CPT 0 0 0 3 1 0.130000 0.000000 + 17 CE3 CA 0 0 0 4 1 -0.115000 0.000000 + 18 HE3 HP 0 0 0 4 1 0.115000 0.000000 + 19 CZ2 CA 0 0 0 5 1 -0.115000 0.000000 + 20 HZ2 HP 0 0 0 5 1 0.115000 0.000000 + 21 CZ3 CA 0 0 0 6 1 -0.115000 0.000000 + 22 HZ3 HP 0 0 0 6 1 0.115000 0.000000 + 23 CH2 CA 0 0 0 7 1 -0.115000 0.000000 + 24 HH2 HP 0 0 0 7 1 0.115000 0.000000 + 25 C C 2 1 0 8 1 0.510000 0.000000 + 26 O O 0 0 0 8 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 25 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 11 16 + 11 17 + 12 13 + 12 14 + 14 15 + 14 16 + 16 19 + 17 18 + 17 21 + 19 20 + 19 23 + 21 22 + 21 23 + 23 24 + 25 26 diff --git a/src/data/charmm_s/TYR.frg b/src/data/charmm_s/TYR.frg new file mode 100644 index 0000000..2e78b97 --- /dev/null +++ b/src/data/charmm_s/TYR.frg @@ -0,0 +1,45 @@ +$TYR + 21 1 1 0 +TYR + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CA 0 0 0 3 1 0.000000 0.000000 + 9 CD1 CA 0 0 0 4 1 -0.115000 0.000000 + 10 HD1 HP 0 0 0 4 1 0.115000 0.000000 + 11 CD2 CA 0 0 0 5 1 -0.115000 0.000000 + 12 HD2 HP 0 0 0 5 1 0.115000 0.000000 + 13 CE1 CA 0 0 0 6 1 -0.115000 0.000000 + 14 HE1 HP 0 0 0 6 1 0.115000 0.000000 + 15 CE2 CA 0 0 0 7 1 -0.115000 0.000000 + 16 HE2 HP 0 0 0 7 1 0.115000 0.000000 + 17 CZ CA 0 0 0 8 1 0.110000 0.000000 + 18 OH OH1 0 0 0 8 1 -0.540000 0.000000 + 19 HH H 0 0 0 8 1 0.430000 0.000000 + 20 C C 2 1 0 9 1 0.510000 0.000000 + 21 O O 0 0 0 9 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 20 + 5 6 + 5 7 + 5 8 + 8 9 + 8 11 + 9 10 + 9 13 + 11 12 + 11 15 + 13 14 + 13 17 + 15 16 + 15 17 + 17 18 + 18 19 + 20 21 diff --git a/src/data/charmm_s/TYR_C.frg b/src/data/charmm_s/TYR_C.frg new file mode 100644 index 0000000..3c9a582 --- /dev/null +++ b/src/data/charmm_s/TYR_C.frg @@ -0,0 +1,47 @@ +$TYR_C + 22 1 1 0 +TYR_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 62HB HA 0 0 0 2 1 0.090000 0.000000 + 73HB HA 0 0 0 2 1 0.090000 0.000000 + 8 CG CA 0 0 0 3 1 0.000000 0.000000 + 9 CD1 CA 0 0 0 4 1 -0.115000 0.000000 + 10 HD1 HP 0 0 0 4 1 0.115000 0.000000 + 11 CD2 CA 0 0 0 5 1 -0.115000 0.000000 + 12 HD2 HP 0 0 0 5 1 0.115000 0.000000 + 13 CE1 CA 0 0 0 6 1 -0.115000 0.000000 + 14 HE1 HP 0 0 0 6 1 0.115000 0.000000 + 15 CE2 CA 0 0 0 7 1 -0.115000 0.000000 + 16 HE2 HP 0 0 0 7 1 0.115000 0.000000 + 17 CZ CA 0 0 0 8 1 0.110000 0.000000 + 18 OH OH1 0 0 0 8 1 -0.540000 0.000000 + 19 HH H 0 0 0 8 1 0.430000 0.000000 + 20 C CC 0 0 0 3 1 0.340000 0.000000 + 21 O OC 0 0 0 3 1 -0.670000 0.000000 + 22 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 20 + 5 6 + 5 7 + 5 8 + 8 9 + 8 11 + 9 10 + 9 13 + 11 12 + 11 15 + 13 14 + 13 17 + 15 16 + 15 17 + 17 18 + 18 19 + 20 21 + 20 22 diff --git a/src/data/charmm_s/TYR_N.frg b/src/data/charmm_s/TYR_N.frg new file mode 100644 index 0000000..34b4482 --- /dev/null +++ b/src/data/charmm_s/TYR_N.frg @@ -0,0 +1,49 @@ +$TYR_N + 23 1 1 0 +TYR_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT2 0 0 0 2 1 -0.180000 0.000000 + 82HB HA 0 0 0 2 1 0.090000 0.000000 + 93HB HA 0 0 0 2 1 0.090000 0.000000 + 10 CG CA 0 0 0 3 1 0.000000 0.000000 + 11 CD1 CA 0 0 0 4 1 -0.115000 0.000000 + 12 HD1 HP 0 0 0 4 1 0.115000 0.000000 + 13 CD2 CA 0 0 0 5 1 -0.115000 0.000000 + 14 HD2 HP 0 0 0 5 1 0.115000 0.000000 + 15 CE1 CA 0 0 0 6 1 -0.115000 0.000000 + 16 HE1 HP 0 0 0 6 1 0.115000 0.000000 + 17 CE2 CA 0 0 0 7 1 -0.115000 0.000000 + 18 HE2 HP 0 0 0 7 1 0.115000 0.000000 + 19 CZ CA 0 0 0 8 1 0.110000 0.000000 + 20 OH OH1 0 0 0 8 1 -0.540000 0.000000 + 21 HH H 0 0 0 8 1 0.430000 0.000000 + 22 C C 2 1 0 9 1 0.510000 0.000000 + 23 O O 0 0 0 9 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 22 + 7 8 + 7 9 + 7 10 + 10 11 + 10 13 + 11 12 + 11 15 + 13 14 + 13 17 + 15 16 + 15 19 + 17 18 + 17 19 + 19 20 + 20 21 + 22 23 diff --git a/src/data/charmm_s/VAL.frg b/src/data/charmm_s/VAL.frg new file mode 100644 index 0000000..b8e4ac3 --- /dev/null +++ b/src/data/charmm_s/VAL.frg @@ -0,0 +1,34 @@ +$VAL + 16 1 1 0 +VAL + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT1 0 0 0 2 1 -0.090000 0.000000 + 6 HB HA 0 0 0 2 1 0.090000 0.000000 + 7 CG1 CT3 0 0 0 3 1 -0.270000 0.000000 + 82HG1 HA 0 0 0 3 1 0.090000 0.000000 + 93HG1 HA 0 0 0 3 1 0.090000 0.000000 + 104HG1 HA 0 0 0 3 1 0.090000 0.000000 + 11 CG2 CT3 0 0 0 4 1 -0.270000 0.000000 + 122HG2 HA 0 0 0 4 1 0.090000 0.000000 + 133HG2 HA 0 0 0 4 1 0.090000 0.000000 + 144HG2 HA 0 0 0 4 1 0.090000 0.000000 + 15 C C 2 1 0 5 1 0.510000 0.000000 + 16 O O 0 0 0 5 1 -0.510000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 15 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 12 + 11 13 + 11 14 + 15 16 diff --git a/src/data/charmm_s/VAL_C.frg b/src/data/charmm_s/VAL_C.frg new file mode 100644 index 0000000..928fe56 --- /dev/null +++ b/src/data/charmm_s/VAL_C.frg @@ -0,0 +1,36 @@ +$VAL_C + 17 1 1 0 +VAL_C + 1 N NH1 1 1 0 1 1 -0.470000 0.000000 + 2 H H 0 0 0 1 1 0.310000 0.000000 + 3 CA CT1 0 0 0 1 1 0.070000 0.000000 + 4 HA HB 0 0 0 1 1 0.090000 0.000000 + 5 CB CT1 0 0 0 2 1 -0.090000 0.000000 + 6 HB HA 0 0 0 2 1 0.090000 0.000000 + 7 CG1 CT3 0 0 0 3 1 -0.270000 0.000000 + 82HG1 HA 0 0 0 3 1 0.090000 0.000000 + 93HG1 HA 0 0 0 3 1 0.090000 0.000000 + 104HG1 HA 0 0 0 3 1 0.090000 0.000000 + 11 CG2 CT3 0 0 0 4 1 -0.270000 0.000000 + 122HG2 HA 0 0 0 4 1 0.090000 0.000000 + 133HG2 HA 0 0 0 4 1 0.090000 0.000000 + 144HG2 HA 0 0 0 4 1 0.090000 0.000000 + 15 C CC 0 0 0 3 1 0.340000 0.000000 + 16 O OC 0 0 0 3 1 -0.670000 0.000000 + 17 OXT OC 0 0 0 3 1 -0.670000 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 15 + 5 6 + 5 7 + 5 11 + 7 8 + 7 9 + 7 10 + 11 12 + 11 13 + 11 14 + 15 16 + 15 17 diff --git a/src/data/charmm_s/VAL_N.frg b/src/data/charmm_s/VAL_N.frg new file mode 100644 index 0000000..e73f5d3 --- /dev/null +++ b/src/data/charmm_s/VAL_N.frg @@ -0,0 +1,38 @@ +$VAL_N + 18 1 1 0 +VAL_N + 1 N NH3 0 0 0 1 1 -0.300000 0.000000 + 22H HC 0 0 0 1 1 0.330000 0.000000 + 33H HC 0 0 0 1 1 0.330000 0.000000 + 44H HC 0 0 0 1 1 0.330000 0.000000 + 5 CA CT1 0 0 0 1 1 0.210000 0.000000 + 6 HA HB 0 0 0 1 1 0.100000 0.000000 + 7 CB CT1 0 0 0 2 1 -0.090000 0.000000 + 8 HB HA 0 0 0 2 1 0.090000 0.000000 + 9 CG1 CT3 0 0 0 3 1 -0.270000 0.000000 + 102HG1 HA 0 0 0 3 1 0.090000 0.000000 + 113HG1 HA 0 0 0 3 1 0.090000 0.000000 + 124HG1 HA 0 0 0 3 1 0.090000 0.000000 + 13 CG2 CT3 0 0 0 4 1 -0.270000 0.000000 + 142HG2 HA 0 0 0 4 1 0.090000 0.000000 + 153HG2 HA 0 0 0 4 1 0.090000 0.000000 + 164HG2 HA 0 0 0 4 1 0.090000 0.000000 + 17 C C 2 1 0 5 1 0.510000 0.000000 + 18 O O 0 0 0 5 1 -0.510000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 17 + 7 8 + 7 9 + 7 13 + 9 10 + 9 11 + 9 12 + 13 14 + 13 15 + 13 16 + 17 18 diff --git a/src/data/charmm_s/ZN2.frg b/src/data/charmm_s/ZN2.frg new file mode 100644 index 0000000..0b7245b --- /dev/null +++ b/src/data/charmm_s/ZN2.frg @@ -0,0 +1,4 @@ +$ZN2 + 1 1 1 0 +ZN2 + 1 ZN ZN 0 0 0 1 1 2.000000 0.000000 diff --git a/src/data/charmm_s/charmm.par b/src/data/charmm_s/charmm.par new file mode 100644 index 0000000..98320f4 --- /dev/null +++ b/src/data/charmm_s/charmm.par @@ -0,0 +1,1093 @@ +This is the CHARMM22 standard parameter file for ARGOS 7.0 +Electrostatic 1-4 scaling factor 1.000000 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +C 12.01100 4.60240E-01 2.00000E-01 1 1111111111 + 6 4.60240E-01 2.00000E-01 +CA 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +CC 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CD 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CE1 12.01100 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-CPH1 3.14159 5.02080E+01 2 +NR3 -CPH2 -NR3 -H 3.14159 5.85760E+00 2 +NY -CA -CY -CPT 3.14159 1.67360E+01 2 +NY -CA -CY -CT2 3.14159 1.46440E+01 2 +NY -CA -CY -HA 3.14159 1.46440E+01 2 +NY -CA -CY -HP 3.14159 1.46440E+01 2 +NY -CPT -CA -CA 3.14159 1.17152E+01 2 +NY -CPT -CA -HA 3.14159 1.67360E+01 2 +NY -CPT -CA -HP 3.14159 1.25520E+01 2 +NY -CPT -CPT -CA 3.14159 4.18400E+01 2 +NY -CPT -CPT -CY 3.14159 2.09200E+01 2 +O -C -CP1 -CP2 3.14159 1.67360E+00 -1 +O -C -CP1 -CP2 0.00000 2.51040E+00 2 +O -C -CP1 -HB 0.00000 1.67360E+00 -1 +O -C -CP1 -HB 0.00000 2.51040E+00 2 +O -C -CP1 -N 0.00000-1.25520E+00 4 +O -C -CT1 -CT1 0.00000 5.85760E+00 1 +O -C -CT1 -CT2 0.00000 5.85760E+00 1 +O -C -CT1 -CT3 0.00000 5.85760E+00 1 +O -C -CT1 -HB 0.00000 0.00000E+00 1 +O -C -CT1 -NH1 0.00000 0.00000E+00 1 +O -C -CT1 -NH3 0.00000 0.00000E+00 1 +O -C -CT2 -CT2 0.00000 5.85760E+00 1 +O -C -CT2 -HA 3.14159 0.00000E+00 3 +O -C -CT2 -HB 0.00000 0.00000E+00 1 +O -C -CT2 -NH1 0.00000 0.00000E+00 1 +O -C -CT2 -NH3 0.00000 0.00000E+00 1 +O -C -CT3 -HA 3.14159 0.00000E+00 3 +O -C -N -CP1 3.14159 1.15060E+01 -2 +O -C -N -CP1 0.00000 1.25520E+00 4 +O -C -N -CP3 3.14159 1.15060E+01 -2 +O -C -N -CP3 0.00000 1.25520E+00 4 +O -C -NH1 -CT1 3.14159 1.04600E+01 2 +O -C -NH1 -CT2 3.14159 1.04600E+01 2 +O -C -NH1 -CT3 3.14159 1.04600E+01 2 +O -C -NH1 -H 3.14159 1.04600E+01 2 +O -CC -CP1 -CP2 3.14159 1.67360E+00 -1 +O -CC -CP1 -CP2 0.00000 2.51040E+00 2 +O -CC -CP1 -HB 0.00000 1.67360E+00 -1 +O -CC -CP1 -HB 0.00000 2.51040E+00 2 +O -CC -CP1 -N 0.00000-1.25520E+00 4 +O -CC -CT2 -HA 3.14159 0.00000E+00 3 +O -CC -NH2 -H 3.14159 5.85760E+00 2 +OB -CD -OS -CT2 3.14159 4.03756E+00 -1 +OB -CD -OS -CT2 3.14159 1.61084E+01 2 +OB -CD -OS -CT3 3.14159 4.03756E+00 -1 +OB -CD -OS -CT3 3.14159 1.61084E+01 2 +OC -CA -CA -CA 3.14159 1.29704E+01 2 +OC -CA -CA -HP 3.14159 1.75728E+01 2 +OC -CC -CP1 -CP2 0.00000 6.69440E-01 3 +OC -CC -CP1 -HB 0.00000 6.69440E-01 3 +OC -CC -CP1 -N 0.00000 6.69440E-01 3 +OC -CC -CP1 -NP 0.00000 6.69440E-01 3 +OC -CC -CT1 -NH3 3.14159 1.33888E+01 2 +OC -CC -CT2 -NH3 3.14159 1.33888E+01 2 +OH1 -CA -CA -CA 3.14159 1.29704E+01 2 +OH1 -CA -CA -HP 3.14159 1.75728E+01 2 +S -CT2 -CT2 -HA 0.00000 4.18400E-02 3 +SM -CT2 -CT2 -HA 0.00000 4.18400E-02 3 +SM -SM -CT2 -CT1 0.00000 1.29704E+00 3 +SM -SM -CT2 -CT2 0.00000 1.29704E+00 3 +SM -SM -CT2 -HA 0.00000 6.61072E-01 3 +SM -SM -CT3 -HA 0.00000 6.61072E-01 3 +SS -CS -CT3 -HA 0.00000 6.27600E-01 3 + -C -C - 3.14159 1.67360E+01 2 + -C -NC2 - 3.14159 9.41400E+00 2 + -CD -OH1 - 3.14159 8.57720E+00 2 + -CD -OS - 3.14159 8.57720E+00 2 + -CE1 -CE1 - 3.14159 2.17568E+01 2 + -CE2 -CE2 - 3.14159 2.05016E+01 2 + -CP1 -C - 3.14159 0.00000E+00 6 + -CP1 -CC - 3.14159 0.00000E+00 6 + -CP1 -CD - 3.14159 0.00000E+00 6 + -CP1 -CP2 - 0.00000 5.85760E-01 3 + -CP2 -CP2 - 0.00000 6.69440E-01 3 + -CP3 -CP2 - 0.00000 5.85760E-01 3 + -CPA -CPB - 0.00000 0.00000E+00 2 + -CPA -CPM - 0.00000 0.00000E+00 2 + -CPB -C - 3.14159 1.25520E+01 2 + -CPB -CPB - 0.00000 0.00000E+00 2 + -CPB -CT2 - 0.00000 0.00000E+00 6 + -CPB -CT3 - 0.00000 0.00000E+00 6 + -CPT -CPT - 3.14159 0.00000E+00 2 + -CT1 -CC - 3.14159 2.09200E-01 6 + -CT1 -CD - 3.14159 0.00000E+00 6 + -CT1 -CT1 - 0.00000 8.36800E-01 3 + -CT1 -CT2 - 0.00000 8.36800E-01 3 + -CT1 -CT3 - 0.00000 8.36800E-01 3 + -CT1 -NH3 - 0.00000 4.18400E-01 3 + -CT1 -OH1 - 0.00000 5.85760E-01 3 + -CT1 -OS - 0.00000-4.18400E-01 3 + -CT2 -CA - 0.00000 0.00000E+00 6 + -CT2 -CC - 3.14159 2.09200E-01 6 + -CT2 -CD - 3.14159 0.00000E+00 6 + -CT2 -CT2 - 0.00000 8.15880E-01 3 + -CT2 -CT3 - 0.00000 6.69440E-01 3 + -CT2 -NC2 - 3.14159 0.00000E+00 6 + -CT2 -NH3 - 0.00000 4.18400E-01 3 + -CT2 -OH1 - 0.00000 5.85760E-01 3 + -CT2 -OS - 0.00000-4.18400E-01 3 + -CT3 -CA - 0.00000 0.00000E+00 6 + -CT3 -CC - 3.14159 2.09200E-01 6 + -CT3 -CD - 3.14159 0.00000E+00 6 + -CT3 -CT3 - 0.00000 6.48520E-01 3 + -CT3 -NC2 - 3.14159 0.00000E+00 6 + -CT3 -NH2 - 0.00000 4.60240E-01 3 + -CT3 -NH3 - 0.00000 3.76560E-01 3 + -CT3 -OH1 - 0.00000 5.85760E-01 3 + -CT3 -OS - 0.00000-4.18400E-01 3 + -FE -CM - 0.00000 2.09200E-01 4 + -FE -NPH - 0.00000 0.00000E+00 2 + -FE -OM - 0.00000 0.00000E+00 4 + -NPH -CPA - 0.00000 0.00000E+00 2 +Improper dihedrals +CPB -CPA -NPH -CPA 0.00000 1.74054E+02 +CPB - - -C 0.00000 7.53120E+02 +CT2 - - -CPB 0.00000 7.53120E+02 +CT3 - - -CPB 0.00000 7.53120E+02 +HA -C -C -HA 0.00000 1.67360E+02 +HA -CPA -CPA -CPM 0.00000 2.46019E+02 +HA -CPB -C -C 0.00000 1.67360E+02 +HA -HA -C -C 3.14159 1.67360E+02 +HA2 -HA2 -CE2 -CE2 0.00000 2.51040E+01 +HR1 -NR1 -NR2 -CPH2 0.00000 4.18400E+00 +HR1 -NR2 -NR1 -CPH2 0.00000 4.18400E+00 +HR3 -CPH1 -NR1 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR2 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR3 -CPH1 0.00000 8.36800E+00 +HR3 -NR1 -CPH1 -CPH1 0.00000 4.18400E+00 +HR3 -NR2 -CPH1 -CPH1 0.00000 4.18400E+00 +N -C -CP1 -CP3 0.00000 0.00000E+00 +NC2 - - -C 0.00000 3.34720E+02 +NH1 - - -H 0.00000 1.67360E+02 +NH2 - - -H 0.00000 3.34720E+01 +NPH -CPA -CPA -FE 0.00000 1.14976E+03 +NPH -CPA -CPB -CPB 0.00000 3.39741E+02 +NPH -CPA -CPM -CPA 0.00000 1.53134E+02 +NPH -CPM -CPB -CPA 0.00000 2.73634E+02 +NR1 -CPH1 -CPH2 -H 0.00000 3.76560E+00 +NR1 -CPH2 -CPH1 -H 0.00000 3.76560E+00 +NR3 -CPH1 -CPH2 -H 0.00000 1.00416E+01 +NR3 -CPH2 -CPH1 -H 0.00000 1.00416E+01 +NY -CA -CY -CPT 0.00000 8.36800E+02 +O -CP1 -NH2 -CC 0.00000 3.76560E+02 +O -CT1 -NH2 -CC 0.00000 3.76560E+02 +O -CT2 -NH2 -CC 0.00000 3.76560E+02 +O -CT3 -NH2 -CC 0.00000 3.76560E+02 +O -HA -NH2 -CC 0.00000 3.76560E+02 +O -N -CT2 -CC 0.00000 1.00416E+03 +O -NH2 -CP1 -CC 0.00000 3.76560E+02 +O -NH2 -CT1 -CC 0.00000 3.76560E+02 +O -NH2 -CT2 -CC 0.00000 3.76560E+02 +O -NH2 -CT3 -CC 0.00000 3.76560E+02 +O -NH2 -HA -CC 0.00000 3.76560E+02 +O - - -C 0.00000 1.00416E+03 +OB - - -CD 0.00000 8.36800E+02 +OC - - -CC 0.00000 8.03328E+02 diff --git a/src/data/charmm_s/par_all27_na_lipid.par b/src/data/charmm_s/par_all27_na_lipid.par new file mode 100644 index 0000000..bf61667 --- /dev/null +++ b/src/data/charmm_s/par_all27_na_lipid.par @@ -0,0 +1,1792 @@ +CHARMM27 July, 2004 standard Nucleic Acid and Lipids parameter file for ARGOS 7.0 +Electrostatic 1-4 scaling factor 1.000000 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +HT 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN1 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN2 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN3 1.00800 1.92464E-01 1.10000E-01 1 1111111111 + 1 1.92464E-01 1.10000E-01 +HNP 1.00800 1.25520E-01 1.35820E-01 1 1111111111 + 1 1.25520E-01 1.35820E-01 +HN3B 1.00800 1.92464E-01 9.00000E-02 1 1111111111 + 1 1.92464E-01 9.00000E-02 +HN3C 1.00800 1.25520E-01 1.35820E-01 1 1111111111 + 1 1.25520E-01 1.35820E-01 +HN4 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN5 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN6 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HN7 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HN8 1.00800 1.17152E-01 1.34000E-01 1 1111111111 + 1 1.17152E-01 1.34000E-01 +HN9 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +HNE1 1.00800 1.29704E-01 1.25000E-01 1 1111111111 + 1 1.29704E-01 1.25000E-01 +HNE2 1.00800 1.08784E-01 1.26000E-01 1 1111111111 + 1 1.08784E-01 1.26000E-01 +NN1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN1C 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2B 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2C 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2G 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2U 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3A 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3G 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3I 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN4 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN5 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN6 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +ON1 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +ON1C 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +ON2 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON2B 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON3 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +ON4 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON5 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON6 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON6B 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OT 15.99900 6.36386E-01 1.76820E-01 1 1111111111 + 8 6.36386E-01 1.76820E-01 +CN1 12.01100 4.18400E-01 1.90000E-01 1 1111111111 + 6 4.18400E-01 1.90000E-01 +CN1A 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CN1T 12.01100 4.18400E-01 1.90000E-01 1 1111111111 + 6 4.18400E-01 1.90000E-01 +CN2 12.01100 4.18400E-01 1.90000E-01 1 1111111111 + 6 4.18400E-01 1.90000E-01 +CN3 12.01100 3.76560E-01 1.90000E-01 1 1111111111 + 6 3.76560E-01 1.90000E-01 +CN3A 12.01100 7.53120E-01 1.80000E-01 1 1111111111 + 6 7.53120E-01 1.80000E-01 +CN3B 12.01100 7.53120E-01 1.80000E-01 1 1111111111 + 6 7.53120E-01 1.80000E-01 +CN3C 12.01100 7.53120E-01 1.80000E-01 1 1111111111 + 6 7.53120E-01 1.80000E-01 +CN3D 12.01100 3.76560E-01 1.90000E-01 1 1111111111 + 6 3.76560E-01 1.90000E-01 +CN3T 12.01100 3.76560E-01 1.90000E-01 1 1111111111 + 6 3.76560E-01 1.90000E-01 +CN4 12.01100 3.13800E-01 1.90000E-01 1 1111111111 + 6 3.13800E-01 1.90000E-01 +CN5 12.01100 3.13800E-01 1.90000E-01 1 1111111111 + 6 3.13800E-01 1.90000E-01 +CN5G 12.01100 3.13800E-01 1.90000E-01 1 1111111111 + 6 3.13800E-01 1.90000E-01 +CN7 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN7B 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN7C 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN7D 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN8 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN8B 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN9 12.01100 3.26352E-01 2.04000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CNE1 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CNE2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +CNA 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +CNA2 12.01100 2.92880E-01 1.90000E-01 1 1111111111 + 6 2.92880E-01 1.90000E-01 +CN6 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CN7E 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +FN1 18.99840 3.76560E-01 1.70000E-01 1 1111111111 + 9 3.76560E-01 1.70000E-01 +FNA 18.99840 5.02080E-01 1.70000E-01 1 1111111111 + 9 5.02080E-01 1.70000E-01 +P 30.97400 2.44764E+00 2.15000E-01 1 1111111111 + 15 2.44764E+00 2.15000E-01 +P2 30.97400 2.44764E+00 2.15000E-01 1 1111111111 + 15 2.44764E+00 2.15000E-01 +P3 30.97400 2.44764E+00 2.15000E-01 1 1111111111 + 15 2.44764E+00 2.15000E-01 +CPH1 12.01100 2.09200E-01 1.80000E-01 1 1111111111 + 6 2.09200E-01 1.80000E-01 +CPH2 12.01100 2.09200E-01 1.80000E-01 1 1111111111 + 6 2.09200E-01 1.80000E-01 +NR1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +HR3 1.00800 3.26352E-02 1.46800E-01 1 1111111111 + 1 3.26352E-02 1.46800E-01 +HR1 1.00800 1.92464E-01 9.00000E-02 1 1111111111 + 1 1.92464E-01 9.00000E-02 +SOD 22.98977 1.96230E-01 1.36375E-01 1 1111111111 + 11 1.96230E-01 1.36375E-01 +POT 39.10200 3.64008E-01 1.76375E-01 1 1111111111 + 19 3.64008E-01 1.76375E-01 +CLA 35.45000 6.27600E-01 2.27000E-01 1 1111111111 + 17 6.27600E-01 2.27000E-01 +CAL 40.08000 5.02080E-01 1.36700E-01 1 1111111111 + 20 5.02080E-01 1.36700E-01 +MG 24.30500 6.27600E-02 1.18500E-01 1 1111111111 + 12 6.27600E-02 1.18500E-01 +CES 132.90000 7.94960E-01 2.10000E-01 1 1111111111 + 55 7.94960E-01 2.10000E-01 +ZN 65.37000 1.04600E+00 1.09000E-01 1 1111111111 + 30 1.04600E+00 1.09000E-01 +DUM 0.00000 0.00000E+00 0.00000E+00 1 1111111111 + 0 0.00000E+00 1.00000E-01 +HOL 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 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-CN7 -HN7 0.00000 0.00000E+00 3 +ON5 -CN7C -CN7 -ON2 0.00000 0.00000E+00 3 + -CTL1 -OHL - 0.00000 5.85760E-01 3 + -CTL2 -OHL - 0.00000 5.85760E-01 3 + -CTL3 -OHL - 0.00000 5.85760E-01 3 +OCL -CCL -CTL1 -NH3L 3.14159 1.33888E+01 2 +OBL -CL -CTL2 -HAL2 3.14159 0.00000E+00 6 +OBL -CL -CTL3 -HAL3 3.14159 0.00000E+00 6 +OSL -CL -CTL2 -HAL2 3.14159 0.00000E+00 6 +OSL -CL -CTL3 -HAL3 3.14159 0.00000E+00 6 +OBL -CL -OSL -CTL1 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL1 3.14159 1.61084E+01 2 +OBL -CL -OSL -CTL2 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL2 3.14159 1.61084E+01 2 +OBL -CL -OSL -CTL3 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL3 3.14159 1.61084E+01 2 + -CL -OSL - 3.14159 8.57720E+00 2 + -CTL1 -CCL - 3.14159 2.09200E-01 6 + -CTL2 -CL - 3.14159 2.09200E-01 6 + -CTL3 -CL - 3.14159 2.09200E-01 6 + -CL -OHL - 3.14159 8.57720E+00 2 +HAL2 -CTL2 -CL -OHL 3.14159 0.00000E+00 6 +HAL3 -CTL3 -CL -OHL 3.14159 0.00000E+00 6 +OSL -PL -OSL -CTL2 3.14159 5.02080E+00 -1 +OSL -PL -OSL -CTL2 3.14159 4.18400E-01 -2 +OSL -PL -OSL -CTL2 3.14159 4.18400E-01 3 +O2L -PL -OSL -CTL2 0.00000 4.18400E-01 3 +OSL -PL -OSL -CTL3 3.14159 5.02080E+00 -1 +OSL -PL -OSL -CTL3 3.14159 4.18400E-01 -2 +OSL -PL -OSL -CTL3 3.14159 4.18400E-01 3 +O2L -PL -OSL -CTL3 0.00000 4.18400E-01 3 +OHL -PL -OSL -CTL2 0.00000 3.97480E+00 -2 +OHL -PL -OSL -CTL2 0.00000 2.09200E+00 3 +OHL -PL -OSL -CTL3 0.00000 3.97480E+00 -2 +OHL -PL -OSL -CTL3 0.00000 2.09200E+00 3 + -OHL -PL - 0.00000 1.25520E+00 3 + -CTL1 -OSL - 0.00000 0.00000E+00 3 + -CTL2 -OSL - 0.00000 0.00000E+00 3 + -CTL3 -OSL - 0.00000 0.00000E+00 3 +CTL3 -CTL2 -OSL -CL 3.14159 2.92880E+00 1 +CTL2 -CTL2 -OSL -CL 3.14159 2.92880E+00 1 +CTL3 -CTL1 -OSL -CL 3.14159 2.92880E+00 1 +CTL2 -CTL1 -OSL -CL 3.14159 2.92880E+00 1 +CTL1 -CTL2 -CL -OSL 3.14159-6.27600E-01 -1 +CTL1 -CTL2 -CL -OSL 3.14159 2.21752E+00 2 +CTL3 -CTL2 -CL -OSL 3.14159-6.27600E-01 -1 +CTL3 -CTL2 -CL -OSL 3.14159 2.21752E+00 2 +CTL3 -CTL1 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL3 -CTL1 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL3 -CTL1 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL3 -CTL1 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL1 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL2 -CTL1 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL2 -CTL1 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL2 -CTL1 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL3 -CTL2 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL3 -CTL2 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL3 -CTL2 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL3 -CTL2 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL2 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL2 -CTL2 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL2 -CTL2 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL2 -CTL2 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL2 -CL -OSL 0.00000 2.51040E-01 -4 +CTL2 -CTL2 -CL -OSL 3.14159 4.43504E-01 -3 +CTL2 -CTL2 -CL -OSL 3.14159 1.83678E+00 -2 +CTL2 -CTL2 -CL -OSL 0.00000 6.40152E-01 1 +CTL2 -CTL2 -CL -OBL 3.14159 8.36800E-02 -4 +CTL2 -CTL2 -CL -OBL 3.14159 1.04600E-01 2 +CTL3 -CTL2 -CTL2 -CL 0.00000 4.10032E-01 -4 +CTL3 -CTL2 -CTL2 -CL 3.14159 1.28449E+00 -3 +CTL3 -CTL2 -CTL2 -CL 0.00000 2.76981E+00 -2 +CTL3 -CTL2 -CTL2 -CL 0.00000 2.17150E+00 1 +CTL2 -CTL2 -CTL2 -CL 0.00000 4.10032E-01 -4 +CTL2 -CTL2 -CTL2 -CL 3.14159 1.28449E+00 -3 +CTL2 -CTL2 -CTL2 -CL 0.00000 2.76981E+00 -2 +CTL2 -CTL2 -CTL2 -CL 0.00000 2.17150E+00 1 + -CTL2 -NTL - 0.00000 1.08784E+00 3 + -CTL5 -NTL - 0.00000 9.62320E-01 3 + -CTL1 -NH3L - 0.00000 4.18400E-01 3 + -CTL2 -NH3L - 0.00000 4.18400E-01 3 +NH3L -CTL2 -CTL2 -OHL 3.14159 2.92880E+00 1 +NH3L -CTL2 -CTL2 -OSL 3.14159 2.92880E+00 1 +NTL -CTL2 -CTL2 -OHL 3.14159 1.79912E+01 -1 +NTL -CTL2 -CTL2 -OHL 3.14159-1.67360E+00 3 +NTL -CTL2 -CTL2 -OSL 3.14159 1.38072E+01 -1 +NTL -CTL2 -CTL2 -OSL 3.14159-1.67360E+00 3 + -CTL1 -CTL1 - 0.00000 8.36800E-01 3 + -CTL1 -CTL2 - 0.00000 8.36800E-01 3 + -CTL1 -CTL3 - 0.00000 8.36800E-01 3 + -CTL2 -CTL2 - 0.00000 7.94960E-01 3 + -CTL2 -CTL3 - 0.00000 6.69440E-01 3 + -CTL3 -CTL3 - 0.00000 6.38060E-01 3 +CTL3 -CTL2 -CTL2 -CTL3 0.00000 1.59787E-01 -2 +CTL3 -CTL2 -CTL2 -CTL3 3.14159 1.32968E-01 6 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 6.29734E-01 -2 +CTL2 -CTL2 -CTL2 -CTL3 3.14159 3.40285E-01 -3 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 4.52876E-01 -4 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 8.53159E-01 5 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 2.69868E-01 -2 +CTL2 -CTL2 -CTL2 -CTL2 3.14159 6.26554E-01 -3 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 3.95723E-01 -4 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 4.70742E-01 5 +HAL3 -CTL3 -OSL -SL 0.00000 0.00000E+00 3 +CTL2 -OSL -SL -O2L 0.00000 0.00000E+00 3 +CTL3 -OSL -SL -O2L 0.00000 0.00000E+00 3 +HEL1 -CEL1 -CEL1 -HEL1 3.14159 4.18400E+00 2 +CTL3 -CEL1 -CEL1 -HEL1 3.14159 4.18400E+00 2 + -CEL1 -CEL1 - 3.14159 1.88280E+00 -1 + -CEL1 -CEL1 - 3.14159 3.55640E+01 2 + -CEL2 -CEL2 - 3.14159 2.05016E+01 2 +CTL2 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +CTL3 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +HEL1 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +CEL1 -CEL1 -CTL2 -HAL2 3.14159 1.25520E+00 3 +CEL1 -CEL1 -CTL3 -HAL3 3.14159 1.25520E+00 3 +CEL1 -CEL1 -CTL2 -CTL3 3.14159 3.76560E+00 -1 +CEL1 -CEL1 -CTL2 -CTL3 3.14159 8.36800E-01 2 +CEL1 -CEL1 -CTL2 -CTL2 3.14159 2.51040E+00 1 +CEL1 -CTL2 -CTL2 -CTL3 1.57080 1.25520E+00 -1 +CEL1 -CTL2 -CTL2 -CTL3 0.00000 8.36800E-01 -2 +CEL1 -CTL2 -CTL2 -CTL3 3.14159 1.04600E+00 3 +CEL1 -CTL2 -CTL2 -CTL2 1.57080 1.25520E+00 -1 +CEL1 -CTL2 -CTL2 -CTL2 0.00000 8.36800E-01 -2 +CEL1 -CTL2 -CTL2 -CTL2 3.14159 1.04600E+00 3 +CEL2 -CEL1 -CTL2 -CTL2 3.14159 2.09200E+00 -1 +CEL2 -CEL1 -CTL2 -CTL2 3.14159 5.43920E+00 3 +CEL2 -CEL1 -CTL2 -CTL3 3.14159 2.09200E+00 -1 +CEL2 -CEL1 -CTL2 -CTL3 3.14159 5.43920E+00 3 +CEL2 -CEL1 -CTL2 -HAL2 0.00000 5.02080E-01 3 +CEL2 -CEL1 -CTL3 -HAL3 3.14159 2.09200E-01 3 +HEL1 -CEL1 -CTL2 -CTL2 0.00000 5.02080E-01 3 +HEL1 -CEL1 -CTL2 -CTL3 0.00000 5.02080E-01 3 +HEL1 -CEL1 -CTL2 -HAL2 0.00000 0.00000E+00 3 +HEL1 -CEL1 -CTL3 -HAL3 0.00000 0.00000E+00 3 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 5.02080E+00 -1 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 1.67360E+00 -2 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 5.43920E+00 3 +CEL1 -CTL2 -CEL1 -HEL1 0.00000 0.00000E+00 -2 +CEL1 -CTL2 -CEL1 -HEL1 0.00000 0.00000E+00 3 +CEL1 -CEL1 -CTL2 -CEL1 3.14159 4.18400E+00 -1 +CEL1 -CEL1 -CTL2 -CEL1 0.00000 4.18400E-01 -2 +CEL1 -CEL1 -CTL2 -CEL1 3.14159 1.25520E+00 -3 +CEL1 -CEL1 -CTL2 -CEL1 0.00000 8.36800E-01 4 +Improper dihedrals +HN2 - - -NN2 0.00000 8.36800E+00 +NN2B -CN4 -CN5 -HN2 0.00000 5.85760E+01 +NN2G -CN4 -CN1 -HN2 0.00000 6.69440E+00 +HN1 - - -NN1 0.00000 3.34720E+01 +NN1 -CN2 -HN1 -HN1 0.00000 5.02080E+01 +CN1 - - -ON1 0.00000 7.53120E+02 +CN1T - - -ON1 0.00000 7.53120E+02 +CN1 -NN2G -CN5G -ON1 0.00000 7.53120E+02 +CN1T -NN2B -NN2U -ON1 0.00000 9.20480E+02 +CN1 -NN2U -CN3T -ON1 0.00000 7.53120E+02 +CN1 - - -ON1C 0.00000 6.69440E+02 +CN2 - - -NN1 0.00000 7.53120E+02 +CN2 -NN3G -NN2G -NN1 0.00000 3.34720E+02 +CN2 -NN3A -CN5 -NN1 0.00000 3.34720E+02 +CN2 -NN3 -CN3 -NN1 0.00000 5.02080E+02 +CN4 -NN2G -NN3I -HN3 0.00000 3.26352E+02 +CN9 - - -CN3T 0.00000 1.17152E+02 +CN3 -CN3C -CN8 -HN6 0.00000 1.25520E+02 +HN3B - - -CN3 0.00000 1.25520E+02 +HN3B - - -CN3A 0.00000 1.08784E+02 +HN3B - - -CN3B 0.00000 1.08784E+02 +HN2 -CN3 -CN3B -NN2 0.00000 4.18400E+02 +HN1 -HN1 -CN1A -NN1 0.00000-4.18400E+01 +ON1 - - -CN1A 0.00000 3.34720E+02 +HN3 - - -CN3C 0.00000 4.43504E+02 +HN6 - - -CN3C 0.00000 4.43504E+02 +HN8 -CN3 -CN3 -CN8 0.00000 1.50624E+02 +HR1 -NR1 -NR2 -CPH2 0.00000 4.18400E+00 +HR1 -NR2 -NR1 -CPH2 0.00000 4.18400E+00 +HR3 -CPH1 -NR1 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR2 -CPH1 0.00000 4.18400E+00 +HR3 -NR1 -CPH1 -CPH1 0.00000 4.18400E+00 +HR3 -NR2 -CPH1 -CPH1 0.00000 4.18400E+00 +NR1 -CPH1 -CPH2 -CN7B 0.00000 5.02080E+00 +NR1 -CPH2 -CPH1 -CN7B 0.00000 5.02080E+00 +OBL - - -CL 0.00000 8.36800E+02 +HEL2 -HEL2 -CEL2 -CEL2 0.00000 2.51040E+01 +OCL - - -CL 0.00000 8.03328E+02 +OCL - - -CCL 0.00000 8.03328E+02 +Atom types +# +# Definition of the atom types +# +# This file contains the definition of AMBER atom types in terms of number and +# type of neighbor atoms. +# +# Note that the order in which the definitions are given is important. +# For each atom the last applicable entry in this file will be used, i.e. +# atom type definitions are given in increasing specificity. +# +# Atomic number increased by 200 means singly protonated +# 400 doubly +# 600 triply +# 800 un-protonated +# 1000 one non-hydrogen +# 2000 two non-hydrogens +# 3000 three non-hydrogens +# 4000 four non-hydrogens +# +# Atom number 3500 would signify any unprotonated atom with three non-hydrogens +# +# +# Each entry contains: +# +# 1 a4 atom type name +# +# 2 i7 atomic number +# +# 3 i3 atom saturation : 0 = undetermined, always applies +# 1 = aliphatic; +# 2 = double bond; +# 3 = aromatic; +# +# 4 i5 aliphatic ring : -1 = not in aliphatic ring +# 0 = any +# 1 = in at least one aliphatic ring +# 3 = in 3-membered aliphatic ring +# 4 = in 4-membered aliphatic ring +# 5 = in 5-membered aliphatic ring +# 6 = in 6-membered aliphatic ring +# 56 = junction 5 & 6 membered aliphatic rings +# 66 = junction two 6 membered aliphatic rings +# +# 5 i5 aromatic ring : -1 = not in aromatic ring +# 0 = any +# 1 = in at least one aromatic ring +# 5 = in 5-membered aromatic ring +# 6 = in 6-membered aromatic ring +# 56 = junction 5 & 6 membered aromatic rings +# 66 = junction two 6 membered aromatic rings +# 666 = junction three 6 membered aromatic rings +# +# 6 i3 number of neighbors : -1 = no neighbors +# 0 = any number of neighbors +# +# 7 i7 atom num neighbor 1 +# +# 8 i3 num n1 neighbors 0 = any number of neighbors +# +# 9 i7 atom num neighb n11 +# +# 10 i7 atom num neighb n12 +# +# 11 i7 atom num neighb n13 +# +# 12 i7 atom num neighbor 2 +# +# 13 i3 num n2 neighbors 0 = any number of neighbors +# +# 14 i7 atom num neighb n21 +# +# 15 i7 atom num neighb n22 +# +# 16 i7 atom num neighb n23 +# +# 17 i7 atom num neighbor 3 +# +# 18 i3 num n3 neighbors 0 = any number of neighbors +# +# 19 i7 atom num neighb n31 +# +# 20 i7 atom num neighb n32 +# +# 21 i7 atom num neighb n33 +# +# +End diff --git a/src/data/charmm_s/par_all27_prot_lipid.par b/src/data/charmm_s/par_all27_prot_lipid.par new file mode 100644 index 0000000..dd5e65a --- /dev/null +++ b/src/data/charmm_s/par_all27_prot_lipid.par @@ -0,0 +1,1640 @@ +CHARMM22 July, 2003 standard Proteins and Lipids parameter file for ARGOS 7.0 +Electrostatic 1-4 scaling factor 1.000000 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +C 12.01100 4.60240E-01 2.00000E-01 1 1111111111 + 6 4.60240E-01 2.00000E-01 +CA 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +CC 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CD 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CE1 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CE2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +CM 12.01100 4.60240E-01 2.10000E-01 1 1111111111 + 6 4.60240E-01 2.10000E-01 +CP1 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CP2 12.01100 2.30120E-01 2.17500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CP3 12.01100 2.30120E-01 2.17500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CPA 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.80000E-01 +CPB 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.80000E-01 +CPH1 12.01100 2.09200E-01 1.80000E-01 1 1111111111 + 6 2.09200E-01 1.80000E-01 +CPH2 12.01100 2.09200E-01 1.80000E-01 1 1111111111 + 6 2.09200E-01 1.80000E-01 +CPM 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.80000E-01 +CPT 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.90000E-01 +CS 12.01100 4.60240E-01 2.20000E-01 1 1111111111 + 6 4.60240E-01 2.20000E-01 +CST 12.01100 2.42672E-01 1.56300E-01 1 1111111111 + 6 2.42672E-01 1.56300E-01 +CT1 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT2 12.01100 2.30120E-01 2.17500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT3 12.01100 3.34720E-01 2.06000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CY 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +CT 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT1x 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT2x 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT3x 12.01100 3.26352E-01 2.04000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +H 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HA 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HE1 1.00800 1.29704E-01 1.25000E-01 1 1111111111 + 1 1.29704E-01 1.25000E-01 +HE2 1.00800 1.08784E-01 1.26000E-01 1 1111111111 + 1 1.08784E-01 1.26000E-01 +HB 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HC 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HP 1.00800 1.25520E-01 1.35820E-01 1 1111111111 + 1 1.25520E-01 1.35820E-01 +HR1 1.00800 1.92464E-01 9.00000E-02 1 1111111111 + 1 1.92464E-01 9.00000E-02 +HR2 1.00800 1.92464E-01 7.00000E-02 1 1111111111 + 1 1.92464E-01 7.00000E-02 +HR3 1.00800 3.26352E-02 1.46800E-01 1 1111111111 + 1 3.26352E-02 1.46800E-01 +HS 1.00800 4.18400E-01 4.50000E-02 1 1111111111 + 1 4.18400E-01 4.50000E-02 +HT 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HA1 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HA2 1.00800 1.17152E-01 1.34000E-01 1 1111111111 + 1 1.17152E-01 1.34000E-01 +HA3 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +N 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 4.18400E-04 1.85000E-01 +NC2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NH1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.55000E-01 +NH2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NH3 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NP 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NPH 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR3 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NY 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +O 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +OB 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +OC 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +OH1 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OM 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +OS 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OST 15.99900 6.90360E-01 1.69200E-01 1 1111111111 + 8 6.90360E-01 1.69200E-01 +OT 15.99900 6.36386E-01 1.76820E-01 1 1111111111 + 8 6.36386E-01 1.76820E-01 +S 32.06000 1.88280E+00 2.00000E-01 1 1111111111 + 16 1.88280E+00 2.00000E-01 +SM 32.06000 1.58992E+00 1.97500E-01 1 1111111111 + 16 1.58992E+00 1.97500E-01 +SS 32.06000 1.96648E+00 2.20000E-01 1 1111111111 + 16 1.96648E+00 2.20000E-01 +SOD 22.98977 1.96230E-01 1.36375E-01 1 1111111111 + 11 1.96230E-01 1.36375E-01 +POT 39.10200 3.64008E-01 1.76375E-01 1 1111111111 + 19 3.64008E-01 1.76375E-01 +CLA 35.45000 6.27600E-01 2.27000E-01 1 1111111111 + 17 6.27600E-01 2.27000E-01 +CAL 40.08000 5.02080E-01 1.36700E-01 1 1111111111 + 20 5.02080E-01 1.36700E-01 +MG 24.30500 6.27600E-02 1.18500E-01 1 1111111111 + 12 6.27600E-02 1.18500E-01 +CES 132.90000 7.94960E-01 2.10000E-01 1 1111111111 + 55 7.94960E-01 2.10000E-01 +ZN 65.37000 1.04600E+00 1.09000E-01 1 1111111111 + 30 1.04600E+00 1.09000E-01 +FE 55.84700 0.00000E+00 6.50000E-02 1 1111111111 + 26 0.00000E+00 6.50000E-02 +HE 4.00260 8.89937E-02 1.48000E-01 1 1111111111 + 2 8.89937E-02 1.48000E-01 +NE 20.17970 3.59824E-01 1.53000E-01 1 1111111111 + 10 3.59824E-01 1.53000E-01 +CLAL 35.45300 1.25520E-01 1.90820E-01 1 1111111111 + 17 1.25520E-01 1.90820E-01 +DUM 0.00000 0.00000E+00 0.00000E+00 1 1111111111 + 0 0.00000E+00 0.00000E+00 +CAP 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +FA 18.99800 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +CN 12.01100 8.36800E-01 1.75000E-01 1 1111111111 + 6 8.36800E-01 1.75000E-01 +NC 14.00700 2.51040E+00 1.85000E-01 1 1111111111 + 7 2.51040E+00 1.85000E-01 +OCA 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +COA 12.01100 4.60240E-01 2.00000E-01 1 1111111111 + 6 4.60240E-01 2.00000E-01 +CF1 12.01100 2.51040E-01 1.90000E-01 1 1111111111 + 6 2.51040E-01 1.90000E-01 +CF2 12.01100 1.75728E-01 2.05000E-01 1 1111111111 + 6 1.75728E-01 2.05000E-01 +CF3 12.01100 8.36800E-02 2.30000E-01 1 1111111111 + 6 8.36800E-02 2.30000E-01 +HF1 1.00800 1.17152E-01 1.32000E-01 1 1111111111 + 1 1.17152E-01 1.32000E-01 +HF2 1.00800 1.25520E-01 1.30000E-01 1 1111111111 + 1 1.25520E-01 1.30000E-01 +F1 18.99800 5.64840E-01 1.63000E-01 1 1111111111 + 8 5.64840E-01 1.63000E-01 +F2 18.99800 4.39320E-01 1.63000E-01 1 1111111111 + 8 4.39320E-01 1.63000E-01 +F3 18.99800 4.05848E-01 1.60000E-01 1 1111111111 + 8 4.05848E-01 1.60000E-01 +C3 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 8.36800E-02 2.27500E-01 +CC1A 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CC1B 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CC2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +NS1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NS2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +HOL 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HAL1 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HAL2 1.00800 1.17152E-01 1.34000E-01 1 1111111111 + 1 1.17152E-01 1.34000E-01 +HAl3 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +HBL 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HCL 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HL 1.00800 1.92464E-01 7.00000E-02 1 1111111111 + 1 1.92464E-01 7.00000E-02 +HEL1 1.00800 1.29704E-01 1.25000E-01 1 1111111111 + 1 1.29704E-01 1.25000E-01 +HEL2 1.00800 1.08784E-01 1.26000E-01 1 1111111111 + 1 1.08784E-01 1.26000E-01 +CL 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CCL 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CTL1 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CTL2 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CTL3 12.01100 3.26352E-01 2.04000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CTL5 12.01100 3.34720E-01 2.06000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CEL1 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CEL2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +OBL 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +OCL 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +O2L 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +OHL 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OSL 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +NH3L 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NTL 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +SL 32.06000 1.96648E+00 2.10000E-01 1 1111111111 + 16 1.96648E+00 2.10000E-01 +PL 30.97400 2.44764E+00 2.15000E-01 1 1111111111 + 15 2.44764E+00 2.15000E-01 +Cross +Bonds +NH2 -CT1 0.14550 2.00832E+05 +CST -OST 0.11600 7.84885E+05 +SS -FE 0.23200 2.09200E+05 +C -C 0.13350 5.02080E+05 +CA -CA 0.13750 2.55224E+05 +CE1 -CE1 0.13400 3.68192E+05 +CE1 -CE2 0.13420 4.18400E+05 +CE1 -CT2 0.15020 3.05432E+05 +CE1 -CT3 0.15040 3.20494E+05 +CE2 -CE2 0.13300 4.26768E+05 +CP1 -C 0.14900 2.09200E+05 +CP1 -CC 0.14900 2.09200E+05 +CP1 -CD 0.14900 1.67360E+05 +CP2 -CP1 0.15270 1.86188E+05 +CP2 -CP2 0.15370 1.86188E+05 +CP3 -CP2 0.15370 1.86188E+05 +CPB -CE1 0.13800 3.76560E+05 +CPB -CPA 0.14432 2.50873E+05 +CPB -CPB 0.13464 2.85098E+05 +CPH1 -CPH1 0.13600 3.43088E+05 +CPM -CPA 0.13716 3.01248E+05 +CPT -CA 0.13680 2.55224E+05 +CPT -CPT 0.14000 3.01248E+05 +CT1 -C 0.14900 2.09200E+05 +CT1 -CC 0.15220 1.67360E+05 +CT1 -CD 0.15220 1.67360E+05 +CT1 -CT1 0.15000 1.86188E+05 +CT2 -C 0.14900 2.09200E+05 +CT2 -CA 0.14900 1.92464E+05 +CT2 -CC 0.15220 1.67360E+05 +CT2 -CD 0.15220 1.67360E+05 +CT2 -CPB 0.14900 1.92464E+05 +CT2 -CPH1 0.15000 1.92154E+05 +CT2 -CT1 0.15380 1.86188E+05 +CT2 -CT2 0.15300 1.86188E+05 +CT3 -C 0.14900 2.09200E+05 +CT3 -CA 0.14900 1.92464E+05 +CT3 -CC 0.15220 1.67360E+05 +CT3 -CD 0.15220 1.67360E+05 +CT3 -CPB 0.14900 1.92464E+05 +CT3 -CPH1 0.15000 1.92154E+05 +CT3 -CS 0.15310 1.58992E+05 +CT3 -CT1 0.15380 1.86188E+05 +CT3 -CT2 0.15280 1.86188E+05 +CT3 -CT3 0.15300 1.86188E+05 +CY -CA 0.13650 2.92880E+05 +CY -CPT 0.14400 2.92880E+05 +CY -CT2 0.15100 1.92464E+05 +FE -CM 0.19000 2.15894E+05 +FE -CPM 0.33814 0.00000E+00 +H -CD 0.11100 2.76144E+05 +HA -CA 0.10830 2.84512E+05 +HA -CC 0.11000 2.65374E+05 +HA -CP2 0.11110 2.58571E+05 +HA -CP3 0.11110 2.58571E+05 +HA -CPM 0.10900 3.07608E+05 +HA -CS 0.11110 2.51040E+05 +HA -CT1 0.11110 2.58571E+05 +HA -CT2 0.11110 2.58571E+05 +HA -CT3 0.11110 2.69450E+05 +HA -CY 0.10800 2.76144E+05 +HE1 -CE1 0.11000 3.01666E+05 +HE2 -CE2 0.11000 3.05432E+05 +HB -CP1 0.10800 2.76144E+05 +HB -CT1 0.10800 2.76144E+05 +HB -CT2 0.10800 2.76144E+05 +HB -CT3 0.10800 2.76144E+05 +HP -CA 0.10800 2.84512E+05 +HP -CY 0.10800 2.92880E+05 +HR1 -CPH1 0.10830 3.13800E+05 +HR1 -CPH2 0.10900 2.84512E+05 +HR2 -CPH2 0.10700 2.78654E+05 +HR3 -CPH1 0.10830 3.05432E+05 +HT -HT 0.15139 0.00000E+00 +N -C 0.13000 2.17568E+05 +N -CP1 0.14340 2.67776E+05 +N -CP3 0.14550 2.67776E+05 +NC2 -C 0.13650 3.87438E+05 +NC2 -CT2 0.14900 2.18405E+05 +NC2 -CT3 0.14900 2.18405E+05 +NC2 -HC 0.10000 3.80744E+05 +NH1 -C 0.13450 3.09616E+05 +NH1 -CT1 0.14300 2.67776E+05 +NH1 -CT2 0.14300 2.67776E+05 +NH1 -CT3 0.14300 2.67776E+05 +NH1 -H 0.09970 3.68192E+05 +NH1 -HC 0.09800 3.38904E+05 +NH2 -CC 0.13600 3.59824E+05 +NH2 -CT2 0.14550 2.00832E+05 +NH2 -CT3 0.14550 2.00832E+05 +NH2 -H 0.10000 4.01664E+05 +NH2 -HC 0.10000 3.84928E+05 +NH3 -CT1 0.14800 1.67360E+05 +NH3 -CT2 0.14800 1.67360E+05 +NH3 -CT3 0.14800 1.67360E+05 +NH3 -HC 0.10400 3.37230E+05 +NP -CP1 0.14850 2.67776E+05 +NP -CP3 0.15020 2.67776E+05 +NP -HC 0.10060 3.84928E+05 +NPH -CPA 0.13757 3.15641E+05 +NPH -FE 0.19580 2.26103E+05 +NR1 -CPH1 0.13800 3.34720E+05 +NR1 -CPH2 0.13600 3.34720E+05 +NR1 -H 0.10000 3.89949E+05 +NR2 -CPH1 0.13800 3.34720E+05 +NR2 -CPH2 0.13200 3.34720E+05 +NR2 -FE 0.22000 5.43920E+04 +NR3 -CPH1 0.13700 3.17984E+05 +NR3 -CPH2 0.13200 3.17984E+05 +NR3 -H 0.10000 3.79070E+05 +NY -CA 0.13700 2.25936E+05 +NY -CPT 0.13750 2.25936E+05 +NY -H 0.09760 3.89112E+05 +O -C 0.12300 5.18816E+05 +O -CC 0.12300 5.43920E+05 +OB -CC 0.12200 6.27600E+05 +OB -CD 0.12200 6.27600E+05 +OC -CA 0.12600 4.39320E+05 +OC -CC 0.12600 4.39320E+05 +OC -CT2 0.13300 3.76560E+05 +OC -CT3 0.13300 3.76560E+05 +OH1 -CA 0.14110 2.79742E+05 +OH1 -CD 0.14000 1.92464E+05 +OH1 -CT1 0.14200 3.58150E+05 +OH1 -CT2 0.14200 3.58150E+05 +OH1 -CT3 0.14200 3.58150E+05 +OH1 -H 0.09600 4.56056E+05 +OM -CM 0.11280 9.33032E+05 +OM -FE 0.18000 2.09200E+05 +OM -OM 0.12300 5.02080E+05 +OS -CD 0.13340 1.25520E+05 +OS -CT3 0.14300 2.84512E+05 +OT -HT 0.09572 3.76560E+05 +S -CT2 0.18180 1.65686E+05 +S -CT3 0.18160 2.00832E+05 +S -HS 0.13250 2.30120E+05 +SM -CT2 0.18160 1.79075E+05 +SM -CT3 0.18160 1.79075E+05 +SM -SM 0.20290 1.44766E+05 +SS -CS 0.18360 1.71544E+05 +CTL3 -CL 0.15220 1.67360E+05 +CTL2 -CL 0.15220 1.67360E+05 +CTL1 -CL 0.15220 1.67360E+05 +CTL1 -CCL 0.15220 1.67360E+05 +OBL -CL 0.12200 6.27600E+05 +OCL -CL 0.12600 4.39320E+05 +OCL -CCL 0.12600 4.39320E+05 +OSL -CL 0.13340 1.25520E+05 +OHL -CL 0.14000 1.92464E+05 +HOL -OHL 0.09600 4.56056E+05 +CTL1 -HAL1 0.11110 2.58571E+05 +CTL1 -HBL 0.10800 2.76144E+05 +CTL2 -HAL2 0.11110 2.58571E+05 +CTL3 -HAL3 0.11110 2.69450E+05 +CTL3 -OSL 0.14300 2.84512E+05 +CTL2 -OSL 0.14300 2.84512E+05 +CTL1 -OSL 0.14300 2.84512E+05 +OSL -PL 0.16000 2.25936E+05 +O2L -PL 0.14800 4.85344E+05 +OHL -PL 0.15900 1.98322E+05 +NH3L -HCL 0.10400 3.43088E+05 +NH3L -CTL1 0.14800 1.67360E+05 +NH3L -CTL2 0.15100 2.18405E+05 +NTL -CTL2 0.15100 1.79912E+05 +NTL -CTL5 0.15100 1.79912E+05 +CTL5 -HL 0.10800 2.51040E+05 +CTL2 -HL 0.10800 2.51040E+05 +CTL1 -CTL1 0.15000 1.86188E+05 +CTL1 -CTL2 0.15380 1.86188E+05 +CTL1 -CTL3 0.15380 1.86188E+05 +CTL2 -CTL2 0.15300 1.86188E+05 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1.91114 2.76144E+02 0.21630 2.51040E+02 +HAL3 -CTL3 -CL 1.91114 2.76144E+02 0.21630 2.51040E+02 +CTL2 -CTL1 -CCL 1.88496 4.35136E+02 0.00000 0.00000E+00 +CTL2 -CTL2 -CL 1.88496 4.35136E+02 0.00000 0.00000E+00 +CTL3 -CTL2 -CL 1.88496 4.35136E+02 0.00000 0.00000E+00 +OSL -CL -CTL3 1.90241 4.60240E+02 0.23260 1.67360E+02 +OSL -CL -CTL2 1.90241 4.60240E+02 0.23260 1.67360E+02 +OHL -CL -OBL 2.14675 4.18400E+02 0.22620 1.75728E+03 +OCL -CCL -CTL1 2.05949 3.34720E+02 0.23880 4.18400E+02 +OCL -CL -CTL2 2.05949 3.34720E+02 0.23880 4.18400E+02 +OCL -CL -CTL3 2.05949 3.34720E+02 0.23880 4.18400E+02 +OCL -CL -OCL 2.16421 8.36800E+02 0.22250 5.85760E+02 +OCL -CCL -OCL 2.16421 8.36800E+02 0.22250 5.85760E+02 +OHL -CL -CTL3 1.92859 4.60240E+02 0.00000 0.00000E+00 +OHL -CL -CTL2 1.92859 4.60240E+02 0.00000 0.00000E+00 +HOL -OHL -CL 2.00713 4.60240E+02 0.00000 0.00000E+00 +OSL -CTL1 -CTL2 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL1 -CTL3 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL2 -CTL1 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL2 -CTL2 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL2 -CTL3 1.92161 6.33458E+02 0.00000 0.00000E+00 +HAL2 -CTL2 -HAL2 1.90241 2.97064E+02 0.18020 4.51872E+01 +HAL3 -CTL3 -HAL3 1.89194 2.97064E+02 0.18020 4.51872E+01 +HAL1 -CTL1 -OSL 1.91114 5.02080E+02 0.00000 0.00000E+00 +HAL2 -CTL2 -OSL 1.91114 5.02080E+02 0.00000 0.00000E+00 +HAL3 -CTL3 -OSL 1.91114 5.02080E+02 0.00000 0.00000E+00 +CTL2 -OSL -PL 2.09440 1.67360E+02 0.23300 2.92880E+02 +CTL3 -OSL -PL 2.09440 1.67360E+02 0.23300 2.92880E+02 +HOL -OHL -PL 2.00713 2.51040E+02 0.23000 3.34720E+02 +OSL -PL -OSL 1.82038 6.69440E+02 0.00000 0.00000E+00 +OSL -PL -O2L 1.94779 8.27595E+02 0.00000 0.00000E+00 +OSL -PL -OHL 1.88496 4.02501E+02 0.00000 0.00000E+00 +O2L -PL -O2L 2.09440 1.00416E+03 0.00000 0.00000E+00 +O2L -PL -OHL 1.88897 8.27595E+02 0.00000 0.00000E+00 +NTL -CTL2 -HL 1.91114 3.34720E+02 0.21300 2.25936E+02 +NTL -CTL5 -HL 1.91114 3.34720E+02 0.21300 2.25936E+02 +HL -CTL2 -HL 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0.00000E+00 +CEL1 -CEL1 -CTL3 2.15548 4.01664E+02 0.00000 0.00000E+00 +CEL2 -CEL1 -CTL2 2.19911 4.01664E+02 0.00000 0.00000E+00 +CEL2 -CEL1 -CTL3 2.18515 3.93296E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CEL1 2.08567 4.35136E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CEL2 2.05949 3.51456E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CTL2 2.02458 3.34720E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CTL3 2.04204 1.84096E+02 0.00000 0.00000E+00 +HEL2 -CEL2 -CEL1 2.10312 3.76560E+02 0.00000 0.00000E+00 +HEL2 -CEL2 -CEL2 2.10312 4.64424E+02 0.00000 0.00000E+00 +HEL2 -CEL2 -HEL2 2.07694 1.58992E+02 0.00000 0.00000E+00 +CEL1 -CTL2 -CTL2 1.95826 2.67776E+02 0.00000 0.00000E+00 +CEL1 -CTL2 -CTL3 1.95826 2.67776E+02 0.00000 0.00000E+00 +HAL2 -CTL2 -CEL1 1.94604 3.76560E+02 0.00000 0.00000E+00 +HAL3 -CTL3 -CEL1 1.94604 3.51456E+02 0.00000 0.00000E+00 +CEL1 -CTL2 -CEL1 1.98968 2.51040E+02 0.00000 0.00000E+00 +Proper dihedrals +NH2 -CT1 -C -O 0.00000 0.00000E+00 1 +NH2 -CT1 -C -NH1 0.00000 0.00000E+00 1 +H -NH2 -CT1 -CT1 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-CY -HP 3.14159 1.46440E+01 2 +NY -CPT -CA -CA 3.14159 1.17152E+01 2 +NY -CPT -CA -HA 3.14159 1.67360E+01 2 +NY -CPT -CA -HP 3.14159 1.25520E+01 2 +NY -CPT -CPT -CA 3.14159 4.18400E+01 2 +NY -CPT -CPT -CY 3.14159 2.09200E+01 2 +O -C -CP1 -CP2 3.14159 1.67360E+00 -1 +O -C -CP1 -CP2 0.00000 2.51040E+00 2 +O -C -CP1 -HB 0.00000 1.67360E+00 -1 +O -C -CP1 -HB 0.00000 2.51040E+00 2 +O -C -CP1 -N 0.00000-1.25520E+00 4 +O -C -CT1 -CT1 0.00000 5.85760E+00 1 +O -C -CT1 -CT2 0.00000 5.85760E+00 1 +O -C -CT1 -CT3 0.00000 5.85760E+00 1 +O -C -CT1 -HB 0.00000 0.00000E+00 1 +O -C -CT1 -NH1 0.00000 0.00000E+00 1 +O -C -CT1 -NH3 0.00000 0.00000E+00 1 +O -C -CT2 -CT2 0.00000 5.85760E+00 1 +O -C -CT2 -HA 3.14159 0.00000E+00 3 +O -C -CT2 -HB 0.00000 0.00000E+00 1 +O -C -CT2 -NH1 0.00000 0.00000E+00 1 +O -C -CT2 -NH3 0.00000 0.00000E+00 1 +O -C -CT3 -HA 3.14159 0.00000E+00 3 +O -C -N -CP1 3.14159 1.15060E+01 -2 +O -C -N -CP1 0.00000 1.25520E+00 4 +O -C -N -CP3 3.14159 1.15060E+01 -2 +O -C -N -CP3 0.00000 1.25520E+00 4 +O -C -NH1 -CT1 3.14159 1.04600E+01 2 +O -C -NH1 -CT2 3.14159 1.04600E+01 2 +O -C -NH1 -CT3 3.14159 1.04600E+01 2 +O -C -NH1 -H 3.14159 1.04600E+01 2 +O -CC -CP1 -CP2 3.14159 1.67360E+00 -1 +O -CC -CP1 -CP2 0.00000 2.51040E+00 2 +O -CC -CP1 -HB 0.00000 1.67360E+00 -1 +O -CC -CP1 -HB 0.00000 2.51040E+00 2 +O -CC -CP1 -N 0.00000-1.25520E+00 4 +O -CC -CT2 -HA 3.14159 0.00000E+00 3 +O -CC -NH2 -H 3.14159 5.85760E+00 2 +OB -CD -OS -CT2 3.14159 4.03756E+00 -1 +OB -CD -OS -CT2 3.14159 1.61084E+01 2 +OB -CD -OS -CT3 3.14159 4.03756E+00 -1 +OB -CD -OS -CT3 3.14159 1.61084E+01 2 +OC -CA -CA -CA 3.14159 1.29704E+01 2 +OC -CA -CA -HP 3.14159 1.75728E+01 2 +OC -CC -CP1 -CP2 0.00000 6.69440E-01 3 +OC -CC -CP1 -HB 0.00000 6.69440E-01 3 +OC -CC -CP1 -N 0.00000 6.69440E-01 3 +OC -CC -CP1 -NP 0.00000 6.69440E-01 3 +OC -CC -CT1 -NH3 3.14159 1.33888E+01 2 +OC -CC -CT2 -NH3 3.14159 1.33888E+01 2 +OH1 -CA -CA -CA 3.14159 1.29704E+01 2 +OH1 -CA -CA -HP 3.14159 1.75728E+01 2 +S -CT2 -CT2 -HA 0.00000 4.18400E-02 3 +SM -CT2 -CT2 -HA 0.00000 4.18400E-02 3 +SM -SM -CT2 -CT1 0.00000 1.29704E+00 3 +SM -SM -CT2 -CT2 0.00000 1.29704E+00 3 +SM -SM -CT2 -HA 0.00000 6.61072E-01 3 +SM -SM -CT3 -HA 0.00000 6.61072E-01 3 +SS -CS -CT3 -HA 0.00000 6.27600E-01 3 + -C -NC2 - 3.14159 9.41400E+00 2 + -CD -OH1 - 3.14159 8.57720E+00 2 + -CD -OS - 3.14159 8.57720E+00 2 + -CE1 -CE1 - 0.00000 6.27600E-01 -1 + -CE1 -CE1 - 3.14159 3.55640E+01 2 + -CE2 -CE2 - 3.14159 2.05016E+01 2 + -CP1 -C - 3.14159 0.00000E+00 6 + -CP1 -CC - 3.14159 0.00000E+00 6 + -CP1 -CD - 3.14159 0.00000E+00 6 + -CP1 -CP2 - 0.00000 5.85760E-01 3 + -CP2 -CP2 - 0.00000 6.69440E-01 3 + -CP3 -CP2 - 0.00000 5.85760E-01 3 + -CPA -CPB - 0.00000 0.00000E+00 2 + -CPA -CPM - 0.00000 0.00000E+00 2 + -CPB -CE1 - 3.14159 1.25520E+01 2 + -CPB -CPB - 0.00000 0.00000E+00 2 + -CPB -CT2 - 0.00000 0.00000E+00 6 + -CPB -CT3 - 0.00000 0.00000E+00 6 + -CPT -CPT - 3.14159 0.00000E+00 2 + -CT1 -CC - 3.14159 2.09200E-01 6 + -CT1 -CD - 3.14159 0.00000E+00 6 + -CT1 -CT1 - 0.00000 8.36800E-01 3 + -CT1 -CT2 - 0.00000 8.36800E-01 3 + -CT1 -CT3 - 0.00000 8.36800E-01 3 + -CT1 -NH3 - 0.00000 4.18400E-01 3 + -CT1 -OH1 - 0.00000 5.85760E-01 3 + -CT1 -OS - 0.00000-4.18400E-01 3 + -CT2 -CA - 0.00000 0.00000E+00 6 + -CT2 -CC - 3.14159 2.09200E-01 6 + -CT2 -CD - 3.14159 0.00000E+00 6 + -CT2 -CT2 - 0.00000 8.15880E-01 3 + -CT2 -CT3 - 0.00000 6.69440E-01 3 + -CT2 -NC2 - 3.14159 0.00000E+00 6 + -CT2 -NH3 - 0.00000 4.18400E-01 3 + -CT2 -OH1 - 0.00000 5.85760E-01 3 + -CT2 -OS - 0.00000-4.18400E-01 3 + -CT3 -CA - 0.00000 0.00000E+00 6 + -CT3 -CC - 3.14159 2.09200E-01 6 + -CT3 -CD - 3.14159 0.00000E+00 6 + -CT3 -CT3 - 0.00000 6.48520E-01 3 + -CT3 -NC2 - 3.14159 0.00000E+00 6 + -CT3 -NH2 - 0.00000 4.60240E-01 3 + -CT3 -NH3 - 0.00000 3.76560E-01 3 + -CT3 -OH1 - 0.00000 5.85760E-01 3 + -CT3 -OS - 0.00000-4.18400E-01 3 + -FE -CM - 0.00000 2.09200E-01 4 + -FE -NPH - 0.00000 0.00000E+00 2 + -FE -NR2 - 0.00000 2.09200E-01 4 + -FE -OM - 0.00000 0.00000E+00 4 + -NPH -CPA - 0.00000 0.00000E+00 2 + -CTL1 -OHL - 0.00000 5.85760E-01 3 + -CTL2 -OHL - 0.00000 5.85760E-01 3 + -CTL3 -OHL - 0.00000 5.85760E-01 3 +OCL -CCL -CTL1 -NH3L 3.14159 1.33888E+01 2 +OBL -CL -CTL2 -HAL2 3.14159 0.00000E+00 6 +OBL -CL -CTL3 -HAL3 3.14159 0.00000E+00 6 +OSL -CL -CTL2 -HAL2 3.14159 0.00000E+00 6 +OSL -CL -CTL3 -HAL3 3.14159 0.00000E+00 6 +OBL -CL -OSL -CTL1 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL1 3.14159 1.61084E+01 2 +OBL -CL -OSL -CTL2 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL2 3.14159 1.61084E+01 2 +OBL -CL -OSL -CTL3 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL3 3.14159 1.61084E+01 2 + -CL -OSL - 3.14159 8.57720E+00 2 + -CTL1 -CCL - 3.14159 2.09200E-01 6 + -CTL2 -CL - 3.14159 2.09200E-01 6 + -CTL3 -CL - 3.14159 2.09200E-01 6 + -CL -OHL - 3.14159 8.57720E+00 2 +HAL2 -CTL2 -CL -OHL 3.14159 0.00000E+00 6 +HAL3 -CTL3 -CL -OHL 3.14159 0.00000E+00 6 +OSL -PL -OSL -CTL2 3.14159 5.02080E+00 -1 +OSL -PL -OSL -CTL2 3.14159 4.18400E-01 -2 +OSL -PL -OSL -CTL2 3.14159 4.18400E-01 3 +O2L -PL -OSL -CTL2 0.00000 4.18400E-01 3 +OSL -PL -OSL -CTL3 3.14159 5.02080E+00 -1 +OSL -PL -OSL -CTL3 3.14159 4.18400E-01 -2 +OSL -PL -OSL -CTL3 3.14159 4.18400E-01 3 +O2L -PL -OSL -CTL3 0.00000 4.18400E-01 3 +OHL -PL -OSL -CTL2 0.00000 3.97480E+00 -2 +OHL -PL -OSL -CTL2 0.00000 2.09200E+00 3 +OHL -PL -OSL -CTL3 0.00000 3.97480E+00 -2 +OHL -PL -OSL -CTL3 0.00000 2.09200E+00 3 + -OHL -PL - 0.00000 1.25520E+00 3 + -CTL1 -OSL - 0.00000 0.00000E+00 3 + -CTL2 -OSL - 0.00000 0.00000E+00 3 + -CTL3 -OSL - 0.00000 0.00000E+00 3 +CTL3 -CTL2 -OSL -CL 3.14159 2.92880E+00 1 +CTL2 -CTL2 -OSL -CL 3.14159 2.92880E+00 1 +CTL3 -CTL1 -OSL -CL 3.14159 2.92880E+00 1 +CTL2 -CTL1 -OSL -CL 3.14159 2.92880E+00 1 +CTL1 -CTL2 -CL -OSL 3.14159-6.27600E-01 -1 +CTL1 -CTL2 -CL -OSL 3.14159 2.21752E+00 2 +CTL3 -CTL2 -CL -OSL 3.14159-6.27600E-01 -1 +CTL3 -CTL2 -CL -OSL 3.14159 2.21752E+00 2 +CTL3 -CTL1 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL3 -CTL1 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL3 -CTL1 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL3 -CTL1 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL1 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL2 -CTL1 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL2 -CTL1 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL2 -CTL1 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL3 -CTL2 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL3 -CTL2 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL3 -CTL2 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL3 -CTL2 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL2 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL2 -CTL2 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL2 -CTL2 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL2 -CTL2 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL2 -CL -OSL 0.00000 2.51040E-01 -4 +CTL2 -CTL2 -CL -OSL 3.14159 4.43504E-01 -3 +CTL2 -CTL2 -CL -OSL 3.14159 1.83678E+00 -2 +CTL2 -CTL2 -CL -OSL 0.00000 6.40152E-01 1 +CTL2 -CTL2 -CL -OBL 3.14159 8.36800E-02 -4 +CTL2 -CTL2 -CL -OBL 3.14159 1.04600E-01 2 +CTL3 -CTL2 -CTL2 -CL 0.00000 4.10032E-01 -4 +CTL3 -CTL2 -CTL2 -CL 3.14159 1.28449E+00 -3 +CTL3 -CTL2 -CTL2 -CL 0.00000 2.76981E+00 -2 +CTL3 -CTL2 -CTL2 -CL 0.00000 2.17150E+00 1 +CTL2 -CTL2 -CTL2 -CL 0.00000 4.10032E-01 -4 +CTL2 -CTL2 -CTL2 -CL 3.14159 1.28449E+00 -3 +CTL2 -CTL2 -CTL2 -CL 0.00000 2.76981E+00 -2 +CTL2 -CTL2 -CTL2 -CL 0.00000 2.17150E+00 1 + -CTL2 -NTL - 0.00000 1.08784E+00 3 + -CTL5 -NTL - 0.00000 9.62320E-01 3 + -CTL1 -NH3L - 0.00000 4.18400E-01 3 + -CTL2 -NH3L - 0.00000 4.18400E-01 3 +NH3L -CTL2 -CTL2 -OHL 3.14159 2.92880E+00 1 +NH3L -CTL2 -CTL2 -OSL 3.14159 2.92880E+00 1 +NTL -CTL2 -CTL2 -OHL 3.14159 1.79912E+01 -1 +NTL -CTL2 -CTL2 -OHL 3.14159-1.67360E+00 3 +NTL -CTL2 -CTL2 -OSL 3.14159 1.38072E+01 -1 +NTL -CTL2 -CTL2 -OSL 3.14159-1.67360E+00 3 + -CTL1 -CTL1 - 0.00000 8.36800E-01 3 + -CTL1 -CTL2 - 0.00000 8.36800E-01 3 + -CTL1 -CTL3 - 0.00000 8.36800E-01 3 + -CTL2 -CTL2 - 0.00000 7.94960E-01 3 + -CTL2 -CTL3 - 0.00000 6.69440E-01 3 + -CTL3 -CTL3 - 0.00000 6.38060E-01 3 +CTL3 -CTL2 -CTL2 -CTL3 0.00000 1.59787E-01 -2 +CTL3 -CTL2 -CTL2 -CTL3 3.14159 1.32968E-01 6 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 6.29734E-01 -2 +CTL2 -CTL2 -CTL2 -CTL3 3.14159 3.40285E-01 -3 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 4.52876E-01 -4 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 8.53159E-01 5 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 2.69868E-01 -2 +CTL2 -CTL2 -CTL2 -CTL2 3.14159 6.26554E-01 -3 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 3.95723E-01 -4 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 4.70742E-01 5 +HAL3 -CTL3 -OSL -SL 0.00000 0.00000E+00 3 +CTL2 -OSL -SL -O2L 0.00000 0.00000E+00 3 +CTL3 -OSL -SL -O2L 0.00000 0.00000E+00 3 +HEL1 -CEL1 -CEL1 -HEL1 3.14159 4.18400E+00 2 +CTL3 -CEL1 -CEL1 -HEL1 3.14159 4.18400E+00 2 + -CEL1 -CEL1 - 3.14159 1.88280E+00 -1 + -CEL1 -CEL1 - 3.14159 3.55640E+01 2 + -CEL2 -CEL2 - 3.14159 2.05016E+01 2 +CTL2 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +CTL3 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +HEL1 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +CEL1 -CEL1 -CTL2 -HAL2 3.14159 1.25520E+00 3 +CEL1 -CEL1 -CTL3 -HAL3 3.14159 1.25520E+00 3 +CEL1 -CEL1 -CTL2 -CTL3 3.14159 3.76560E+00 -1 +CEL1 -CEL1 -CTL2 -CTL3 3.14159 8.36800E-01 2 +CEL1 -CEL1 -CTL2 -CTL2 3.14159 2.51040E+00 1 +CEL1 -CTL2 -CTL2 -CTL3 1.57080 1.25520E+00 -1 +CEL1 -CTL2 -CTL2 -CTL3 0.00000 8.36800E-01 -2 +CEL1 -CTL2 -CTL2 -CTL3 3.14159 1.04600E+00 3 +CEL1 -CTL2 -CTL2 -CTL2 1.57080 1.25520E+00 -1 +CEL1 -CTL2 -CTL2 -CTL2 0.00000 8.36800E-01 -2 +CEL1 -CTL2 -CTL2 -CTL2 3.14159 1.04600E+00 3 +CEL2 -CEL1 -CTL2 -CTL2 3.14159 2.09200E+00 -1 +CEL2 -CEL1 -CTL2 -CTL2 3.14159 5.43920E+00 3 +CEL2 -CEL1 -CTL2 -CTL3 3.14159 2.09200E+00 -1 +CEL2 -CEL1 -CTL2 -CTL3 3.14159 5.43920E+00 3 +CEL2 -CEL1 -CTL2 -HAL2 0.00000 5.02080E-01 3 +CEL2 -CEL1 -CTL3 -HAL3 3.14159 2.09200E-01 3 +HEL1 -CEL1 -CTL2 -CTL2 0.00000 5.02080E-01 3 +HEL1 -CEL1 -CTL2 -CTL3 0.00000 5.02080E-01 3 +HEL1 -CEL1 -CTL2 -HAL2 0.00000 0.00000E+00 3 +HEL1 -CEL1 -CTL3 -HAL3 0.00000 0.00000E+00 3 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 5.02080E+00 -1 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 1.67360E+00 -2 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 5.43920E+00 3 +CEL1 -CTL2 -CEL1 -HEL1 0.00000 0.00000E+00 -2 +CEL1 -CTL2 -CEL1 -HEL1 0.00000 0.00000E+00 3 +CEL1 -CEL1 -CTL2 -CEL1 3.14159 4.18400E+00 -1 +CEL1 -CEL1 -CTL2 -CEL1 0.00000 4.18400E-01 -2 +CEL1 -CEL1 -CTL2 -CEL1 3.14159 1.25520E+00 -3 +CEL1 -CEL1 -CTL2 -CEL1 0.00000 8.36800E-01 4 +Improper dihedrals +CPB -CPA -NPH -CPA 0.00000 1.74054E+02 +CPB - - -CE1 0.00000 7.53120E+02 +CT2 - - -CPB 0.00000 7.53120E+02 +CT3 - - -CPB 0.00000 7.53120E+02 +HA -CPA -CPA -CPM 0.00000 2.46019E+02 +HE2 -HE2 -CE2 -CE2 0.00000 2.51040E+01 +HR1 -NR1 -NR2 -CPH2 0.00000 4.18400E+00 +HR1 -NR2 -NR1 -CPH2 0.00000 4.18400E+00 +HR3 -CPH1 -NR1 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR2 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR3 -CPH1 0.00000 8.36800E+00 +HR3 -NR1 -CPH1 -CPH1 0.00000 4.18400E+00 +HR3 -NR2 -CPH1 -CPH1 0.00000 4.18400E+00 +N -C -CP1 -CP3 0.00000 0.00000E+00 +NC2 - - -C 0.00000 3.34720E+02 +NH1 - - -H 0.00000 1.67360E+02 +NH2 - - -H 0.00000 3.34720E+01 +NPH -CPA -CPA -FE 0.00000 1.14976E+03 +NPH -CPA -CPB -CPB 0.00000 3.39741E+02 +NPH -CPA -CPM -CPA 0.00000 1.53134E+02 +NPH -CPM -CPB -CPA 0.00000 2.73634E+02 +NR1 -CPH1 -CPH2 -H 0.00000 3.76560E+00 +NR1 -CPH2 -CPH1 -H 0.00000 3.76560E+00 +NR3 -CPH1 -CPH2 -H 0.00000 1.00416E+01 +NR3 -CPH2 -CPH1 -H 0.00000 1.00416E+01 +NY -CA -CY -CPT 0.00000 8.36800E+02 +O -CP1 -NH2 -CC 0.00000 3.76560E+02 +O -CT1 -NH2 -CC 0.00000 3.76560E+02 +O -CT2 -NH2 -CC 0.00000 3.76560E+02 +O -CT3 -NH2 -CC 0.00000 3.76560E+02 +O -HA -NH2 -CC 0.00000 3.76560E+02 +O -N -CT2 -CC 0.00000 1.00416E+03 +O -NH2 -CP1 -CC 0.00000 3.76560E+02 +O -NH2 -CT1 -CC 0.00000 3.76560E+02 +O -NH2 -CT2 -CC 0.00000 3.76560E+02 +O -NH2 -CT3 -CC 0.00000 3.76560E+02 +O -NH2 -HA -CC 0.00000 3.76560E+02 +O - - -C 0.00000 1.00416E+03 +OB - - -CD 0.00000 8.36800E+02 +OC - - -CC 0.00000 8.03328E+02 +CC - - -CT1 0.00000 8.03328E+02 +CC - - -CT2 0.00000 8.03328E+02 +CC - - -CT3 0.00000 8.03328E+02 +OBL - - -CL 0.00000 8.36800E+02 +HEL2 -HEL2 -CEL2 -CEL2 0.00000 2.51040E+01 +OCL - - -CL 0.00000 8.03328E+02 +OCL - - -CCL 0.00000 8.03328E+02 +Atom types +# +# Definition of the atom types +# +# This file contains the definition of AMBER atom types in terms of number and +# type of neighbor atoms. +# +# Note that the order in which the definitions are given is important. +# For each atom the last applicable entry in this file will be used, i.e. +# atom type definitions are given in increasing specificity. +# +# Atomic number increased by 200 means singly protonated +# 400 doubly +# 600 triply +# 800 un-protonated +# 1000 one non-hydrogen +# 2000 two non-hydrogens +# 3000 three non-hydrogens +# 4000 four non-hydrogens +# +# Atom number 3500 would signify any unprotonated atom with three non-hydrogens +# +# +# Each entry contains: +# +# 1 a4 atom type name +# +# 2 i7 atomic number +# +# 3 i3 atom saturation : 0 = undetermined, always applies +# 1 = aliphatic; +# 2 = double bond; +# 3 = aromatic; +# +# 4 i5 aliphatic ring : -1 = not in aliphatic ring +# 0 = any +# 1 = in at least one aliphatic ring +# 3 = in 3-membered aliphatic ring +# 4 = in 4-membered aliphatic ring +# 5 = in 5-membered aliphatic ring +# 6 = in 6-membered aliphatic ring +# 56 = junction 5 & 6 membered aliphatic rings +# 66 = junction two 6 membered aliphatic rings +# +# 5 i5 aromatic ring : -1 = not in aromatic ring +# 0 = any +# 1 = in at least one aromatic ring +# 5 = in 5-membered aromatic ring +# 6 = in 6-membered aromatic ring +# 56 = junction 5 & 6 membered aromatic rings +# 66 = junction two 6 membered aromatic rings +# 666 = junction three 6 membered aromatic rings +# +# 6 i3 number of neighbors : -1 = no neighbors +# 0 = any number of neighbors +# +# 7 i7 atom num neighbor 1 +# +# 8 i3 num n1 neighbors 0 = any number of neighbors +# +# 9 i7 atom num neighb n11 +# +# 10 i7 atom num neighb n12 +# +# 11 i7 atom num neighb n13 +# +# 12 i7 atom num neighbor 2 +# +# 13 i3 num n2 neighbors 0 = any number of neighbors +# +# 14 i7 atom num neighb n21 +# +# 15 i7 atom num neighb n22 +# +# 16 i7 atom num neighb n23 +# +# 17 i7 atom num neighbor 3 +# +# 18 i3 num n3 neighbors 0 = any number of neighbors +# +# 19 i7 atom num neighb n31 +# +# 20 i7 atom num neighb n32 +# +# 21 i7 atom num neighb n33 +# +# +End diff --git a/src/data/charmm_s/par_all27_prot_na.par b/src/data/charmm_s/par_all27_prot_na.par new file mode 100644 index 0000000..a437bb8 --- /dev/null +++ b/src/data/charmm_s/par_all27_prot_na.par @@ -0,0 +1,2554 @@ +CHARMM22 December, 2003 standard Proteins and Nucleic Acids parameter file for ARGOS 7.0 +Electrostatic 1-4 scaling factor 1.000000 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +C 12.01100 4.60240E-01 2.00000E-01 1 1111111111 + 6 4.60240E-01 2.00000E-01 +CA 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +CC 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CD 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CE1 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CE2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +CM 12.01100 4.60240E-01 2.10000E-01 1 1111111111 + 6 4.60240E-01 2.10000E-01 +CP1 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CP2 12.01100 2.30120E-01 2.17500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CP3 12.01100 2.30120E-01 2.17500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CPA 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.80000E-01 +CPB 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.80000E-01 +CPH1 12.01100 2.09200E-01 1.80000E-01 1 1111111111 + 6 2.09200E-01 1.80000E-01 +CPH2 12.01100 2.09200E-01 1.80000E-01 1 1111111111 + 6 2.09200E-01 1.80000E-01 +CPM 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.80000E-01 +CPT 12.01100 3.76560E-01 1.80000E-01 1 1111111111 + 6 3.76560E-01 1.90000E-01 +CS 12.01100 4.60240E-01 2.20000E-01 1 1111111111 + 6 4.60240E-01 2.20000E-01 +CST 12.01100 2.42672E-01 1.56300E-01 1 1111111111 + 6 2.42672E-01 1.56300E-01 +CT1 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT2 12.01100 2.30120E-01 2.17500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT3 12.01100 3.34720E-01 2.06000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CY 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 6 2.92880E-01 1.99240E-01 +CT 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT1x 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT2x 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CT3x 12.01100 3.26352E-01 2.04000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +H 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HA 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HE1 1.00800 1.29704E-01 1.25000E-01 1 1111111111 + 1 1.29704E-01 1.25000E-01 +HE2 1.00800 1.08784E-01 1.26000E-01 1 1111111111 + 1 1.08784E-01 1.26000E-01 +HB 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HC 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HP 1.00800 1.25520E-01 1.35820E-01 1 1111111111 + 1 1.25520E-01 1.35820E-01 +HR1 1.00800 1.92464E-01 9.00000E-02 1 1111111111 + 1 1.92464E-01 9.00000E-02 +HR2 1.00800 1.92464E-01 7.00000E-02 1 1111111111 + 1 1.92464E-01 7.00000E-02 +HR3 1.00800 3.26352E-02 1.46800E-01 1 1111111111 + 1 3.26352E-02 1.46800E-01 +HS 1.00800 4.18400E-01 4.50000E-02 1 1111111111 + 1 4.18400E-01 4.50000E-02 +HT 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HA1 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HA2 1.00800 1.17152E-01 1.34000E-01 1 1111111111 + 1 1.17152E-01 1.34000E-01 +HA3 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +N 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 4.18400E-04 1.85000E-01 +NC2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NH1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.55000E-01 +NH2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NH3 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NP 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NPH 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NR3 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NY 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +O 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +OB 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +OC 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +OH1 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OM 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +OS 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OST 15.99900 6.90360E-01 1.69200E-01 1 1111111111 + 8 6.90360E-01 1.69200E-01 +OT 15.99900 6.36386E-01 1.76820E-01 1 1111111111 + 8 6.36386E-01 1.76820E-01 +S 32.06000 1.88280E+00 2.00000E-01 1 1111111111 + 16 1.88280E+00 2.00000E-01 +SM 32.06000 1.58992E+00 1.97500E-01 1 1111111111 + 16 1.58992E+00 1.97500E-01 +SP 32.06000 1.88280E+00 2.20000E-01 1 1111111111 + 16 1.88280E+00 2.20000E-01 +SS 32.06000 1.96648E+00 2.20000E-01 1 1111111111 + 16 1.96648E+00 2.20000E-01 +SOD 22.98977 1.96230E-01 1.36375E-01 1 1111111111 + 11 1.96230E-01 1.36375E-01 +POT 39.10200 3.64008E-01 1.76375E-01 1 1111111111 + 19 3.64008E-01 1.76375E-01 +CLA 35.45000 6.27600E-01 2.27000E-01 1 1111111111 + 17 6.27600E-01 2.27000E-01 +CAL 40.08000 5.02080E-01 1.36700E-01 1 1111111111 + 20 5.02080E-01 1.36700E-01 +MG 24.30500 6.27600E-02 1.18500E-01 1 1111111111 + 12 6.27600E-02 1.18500E-01 +CES 132.90000 7.94960E-01 2.10000E-01 1 1111111111 + 55 7.94960E-01 2.10000E-01 +ZN 65.37000 1.04600E+00 1.09000E-01 1 1111111111 + 30 1.04600E+00 1.09000E-01 +FE 55.84700 0.00000E+00 6.50000E-02 1 1111111111 + 26 0.00000E+00 6.50000E-02 +HE 4.00260 8.89937E-02 1.48000E-01 1 1111111111 + 2 8.89937E-02 1.48000E-01 +NE 20.17970 3.59824E-01 1.53000E-01 1 1111111111 + 10 3.59824E-01 1.53000E-01 +CLAL 35.45300 1.25520E-01 1.90820E-01 1 1111111111 + 17 1.25520E-01 1.90820E-01 +DUM 0.00000 0.00000E+00 0.00000E+00 1 1111111111 + 0 0.00000E+00 0.00000E+00 +CAP 12.01100 2.92880E-01 1.99240E-01 1 1111111111 + 12 2.92880E-01 1.99240E-01 +FA 18.99800 5.02080E-01 1.70000E-01 1 1111111111 + 9 5.02080E-01 1.70000E-01 +CN 12.01100 8.36800E-01 1.75000E-01 1 1111111111 + 6 8.36800E-01 1.75000E-01 +NC 14.00700 2.51040E+00 1.85000E-01 1 1111111111 + 7 2.51040E+00 1.85000E-01 +OCA 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +COA 12.01100 4.60240E-01 2.00000E-01 1 1111111111 + 8 4.60240E-01 2.00000E-01 +CF1 12.01100 2.51040E-01 1.90000E-01 1 1111111111 + 6 2.51040E-01 1.90000E-01 +CF2 12.01100 1.75728E-01 2.05000E-01 1 1111111111 + 6 1.75728E-01 2.05000E-01 +CF3 12.01100 8.36800E-02 2.30000E-01 1 1111111111 + 6 8.36800E-02 2.30000E-01 +HF1 1.00800 1.17152E-01 1.32000E-01 1 1111111111 + 1 1.17152E-01 1.32000E-01 +HF2 1.00800 1.25520E-01 1.30000E-01 1 1111111111 + 1 1.25520E-01 1.30000E-01 +F1 18.99800 5.64840E-01 1.63000E-01 1 1111111111 + 9 5.64840E-01 1.63000E-01 +F2 18.99800 4.39320E-01 1.63000E-01 1 1111111111 + 9 4.39320E-01 1.63000E-01 +F3 18.99800 4.05848E-01 1.60000E-01 1 1111111111 + 9 4.05848E-01 1.60000E-01 +C3 15.03500 8.36800E-02 2.27500E-01 1 1111111111 + 6 8.36800E-02 2.27500E-01 +CC1A 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CC1B 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CC2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +NS1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NS2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +HN1 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN2 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN3 1.00800 1.92464E-01 1.10000E-01 1 1111111111 + 1 1.92464E-01 1.10000E-01 +HNP 1.00800 1.25520E-01 1.35820E-01 1 1111111111 + 1 1.25520E-01 1.35820E-01 +HN3B 1.00800 1.92464E-01 9.00000E-02 1 1111111111 + 1 1.92464E-01 9.00000E-02 +HN3C 1.00800 1.25520E-01 1.35820E-01 1 1111111111 + 1 1.25520E-01 1.35820E-01 +HN4 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN5 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HN6 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HN7 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HN8 1.00800 1.17152E-01 1.34000E-01 1 1111111111 + 1 1.17152E-01 1.34000E-01 +HN9 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +HNE1 1.00800 1.29704E-01 1.25000E-01 1 1111111111 + 1 1.29704E-01 1.25000E-01 +HNE2 1.00800 1.08784E-01 1.26000E-01 1 1111111111 + 1 1.08784E-01 1.26000E-01 +NN1 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN1C 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2B 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2C 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2G 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN2U 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3A 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3G 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN3I 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN4 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN5 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NN6 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +ON1 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +ON1C 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +ON2 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON2B 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON3 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +ON4 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON5 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +ON6 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 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+CT3 - - -CPB 0.00000 7.53120E+02 +HA -CPA -CPA -CPM 0.00000 2.46019E+02 +HE2 -HE2 -CE2 -CE2 0.00000 2.51040E+01 +HR1 -NR1 -NR2 -CPH2 0.00000 4.18400E+00 +HR1 -NR2 -NR1 -CPH2 0.00000 4.18400E+00 +HR3 -CPH1 -NR1 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR2 -CPH1 0.00000 4.18400E+00 +HR3 -CPH1 -NR3 -CPH1 0.00000 8.36800E+00 +HR3 -NR1 -CPH1 -CPH1 0.00000 4.18400E+00 +HR3 -NR2 -CPH1 -CPH1 0.00000 4.18400E+00 +N -C -CP1 -CP3 0.00000 0.00000E+00 +NC2 - - -C 0.00000 3.34720E+02 +NH1 - - -H 0.00000 1.67360E+02 +NH2 - - -H 0.00000 3.34720E+01 +NPH -CPA -CPA -FE 0.00000 1.14976E+03 +NPH -CPA -CPB -CPB 0.00000 3.39741E+02 +NPH -CPA -CPM -CPA 0.00000 1.53134E+02 +NPH -CPM -CPB -CPA 0.00000 2.73634E+02 +NR1 -CPH1 -CPH2 -H 0.00000 3.76560E+00 +NR1 -CPH2 -CPH1 -H 0.00000 3.76560E+00 +NR3 -CPH1 -CPH2 -H 0.00000 1.00416E+01 +NR3 -CPH2 -CPH1 -H 0.00000 1.00416E+01 +NY -CA -CY -CPT 0.00000 8.36800E+02 +O -CP1 -NH2 -CC 0.00000 3.76560E+02 +O -CT1 -NH2 -CC 0.00000 3.76560E+02 +O -CT2 -NH2 -CC 0.00000 3.76560E+02 +O -CT3 -NH2 -CC 0.00000 3.76560E+02 +O -HA -NH2 -CC 0.00000 3.76560E+02 +O -N -CT2 -CC 0.00000 1.00416E+03 +O -NH2 -CP1 -CC 0.00000 3.76560E+02 +O -NH2 -CT1 -CC 0.00000 3.76560E+02 +O -NH2 -CT2 -CC 0.00000 3.76560E+02 +O -NH2 -CT3 -CC 0.00000 3.76560E+02 +O -NH2 -HA -CC 0.00000 3.76560E+02 +O - - -C 0.00000 1.00416E+03 +OB - - -CD 0.00000 8.36800E+02 +OC - - -CC 0.00000 8.03328E+02 +CC - - -CT1 0.00000 8.03328E+02 +CC - - -CT2 0.00000 8.03328E+02 +CC - - -CT3 0.00000 8.03328E+02 +HN2 - - -NN2 0.00000 8.36800E+00 +NN2B -CN4 -CN5 -HN2 0.00000 5.85760E+01 +NN2G -CN4 -CN1 -HN2 0.00000 6.69440E+00 +HN1 - - -NN1 0.00000 3.34720E+01 +NN1 -CN2 -HN1 -HN1 0.00000 5.02080E+01 +CN1 - - -ON1 0.00000 7.53120E+02 +CN1T - - -ON1 0.00000 7.53120E+02 +CN1 -NN2G -CN5G -ON1 0.00000 7.53120E+02 +CN1T -NN2B -NN2U -ON1 0.00000 9.20480E+02 +CN1 -NN2U -CN3T -ON1 0.00000 7.53120E+02 +CN1 - - -ON1C 0.00000 6.69440E+02 +CN2 - - -NN1 0.00000 7.53120E+02 +CN2 -NN3G -NN2G -NN1 0.00000 3.34720E+02 +CN2 -NN3A -CN5 -NN1 0.00000 3.34720E+02 +CN2 -NN3 -CN3 -NN1 0.00000 5.02080E+02 +CN4 -NN2G -NN3I -HN3 0.00000 3.26352E+02 +CN9 - - -CN3T 0.00000 1.17152E+02 +CN3 -CN3C -CN8 -HN6 0.00000 1.25520E+02 +HN3B - - -CN3 0.00000 1.25520E+02 +HN3B - - -CN3A 0.00000 1.08784E+02 +HN3B - - -CN3B 0.00000 1.08784E+02 +HN2 -CN3 -CN3B -NN2 0.00000 4.18400E+02 +HN1 -HN1 -CN1A -NN1 0.00000-4.18400E+01 +ON1 - - -CN1A 0.00000 3.34720E+02 +HN3 - - -CN3C 0.00000 4.43504E+02 +HN6 - - -CN3C 0.00000 4.43504E+02 +HN8 -CN3 -CN3 -CN8 0.00000 1.50624E+02 +Atom types +# +# Definition of the atom types +# +# This file contains the definition of AMBER atom types in terms of number and +# type of neighbor atoms. +# +# Note that the order in which the definitions are given is important. +# For each atom the last applicable entry in this file will be used, i.e. +# atom type definitions are given in increasing specificity. +# +# Atomic number increased by 200 means singly protonated +# 400 doubly +# 600 triply +# 800 un-protonated +# 1000 one non-hydrogen +# 2000 two non-hydrogens +# 3000 three non-hydrogens +# 4000 four non-hydrogens +# +# Atom number 3500 would signify any unprotonated atom with three non-hydrogens +# +# +# Each entry contains: +# +# 1 a4 atom type name +# +# 2 i7 atomic number +# +# 3 i3 atom saturation : 0 = undetermined, always applies +# 1 = aliphatic; +# 2 = double bond; +# 3 = aromatic; +# +# 4 i5 aliphatic ring : -1 = not in aliphatic ring +# 0 = any +# 1 = in at least one aliphatic ring +# 3 = in 3-membered aliphatic ring +# 4 = in 4-membered aliphatic ring +# 5 = in 5-membered aliphatic ring +# 6 = in 6-membered aliphatic ring +# 56 = junction 5 & 6 membered aliphatic rings +# 66 = junction two 6 membered aliphatic rings +# +# 5 i5 aromatic ring : -1 = not in aromatic ring +# 0 = any +# 1 = in at least one aromatic ring +# 5 = in 5-membered aromatic ring +# 6 = in 6-membered aromatic ring +# 56 = junction 5 & 6 membered aromatic rings +# 66 = junction two 6 membered aromatic rings +# 666 = junction three 6 membered aromatic rings +# +# 6 i3 number of neighbors : -1 = no neighbors +# 0 = any number of neighbors +# +# 7 i7 atom num neighbor 1 +# +# 8 i3 num n1 neighbors 0 = any number of neighbors +# +# 9 i7 atom num neighb n11 +# +# 10 i7 atom num neighb n12 +# +# 11 i7 atom num neighb n13 +# +# 12 i7 atom num neighbor 2 +# +# 13 i3 num n2 neighbors 0 = any number of neighbors +# +# 14 i7 atom num neighb n21 +# +# 15 i7 atom num neighb n22 +# +# 16 i7 atom num neighb n23 +# +# 17 i7 atom num neighbor 3 +# +# 18 i3 num n3 neighbors 0 = any number of neighbors +# +# 19 i7 atom num neighb n31 +# +# 20 i7 atom num neighb n32 +# +# 21 i7 atom num neighb n33 +# +# +End diff --git a/src/data/charmm_s/par_all32_lipid.par b/src/data/charmm_s/par_all32_lipid.par new file mode 100644 index 0000000..3a22058 --- /dev/null +++ b/src/data/charmm_s/par_all32_lipid.par @@ -0,0 +1,388 @@ +CHARMM27 Lipid Parameter File December, 2003 file for ARGOS 7.0 +Electrostatic 1-4 scaling factor 1.000000 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +HOL 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HAL1 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HAL2 1.00800 1.17152E-01 1.34000E-01 1 1111111111 + 1 1.17152E-01 1.34000E-01 +HAl3 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +HBL 1.00800 9.20480E-02 1.32000E-01 1 1111111111 + 1 9.20480E-02 1.32000E-01 +HCL 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HT 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +HL 1.00800 1.92464E-01 7.00000E-02 1 1111111111 + 1 1.92464E-01 7.00000E-02 +HEL1 1.00800 1.29704E-01 1.25000E-01 1 1111111111 + 1 1.29704E-01 1.25000E-01 +HEL2 1.00800 1.08784E-01 1.26000E-01 1 1111111111 + 1 1.08784E-01 1.26000E-01 +CL 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CCL 12.01100 2.92880E-01 2.00000E-01 1 1111111111 + 6 2.92880E-01 2.00000E-01 +CTL1 12.01100 8.36800E-02 2.27500E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CTL2 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CTL3 12.01100 3.26352E-01 2.04000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CTL5 12.01100 3.34720E-01 2.06000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CEL1 12.01100 2.84512E-01 2.09000E-01 1 1111111111 + 6 2.84512E-01 2.09000E-01 +CEL2 12.01100 2.67776E-01 2.08000E-01 1 1111111111 + 6 2.67776E-01 2.08000E-01 +OBL 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.40000E-01 +OCL 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +O2L 15.99900 5.02080E-01 1.70000E-01 1 1111111111 + 8 5.02080E-01 1.70000E-01 +OHL 15.99900 6.36386E-01 1.77000E-01 1 1111111111 + 8 6.36386E-01 1.77000E-01 +OSL 15.99900 4.18400E-01 1.65000E-01 1 1111111111 + 8 4.18400E-01 1.65000E-01 +OT 15.99900 6.36386E-01 1.76820E-01 1 1111111111 + 8 6.36386E-01 1.76820E-01 +NH3L 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +NTL 14.00700 8.36800E-01 1.85000E-01 1 1111111111 + 7 8.36800E-01 1.85000E-01 +SL 32.06000 1.96648E+00 2.10000E-01 1 1111111111 + 16 1.96648E+00 2.10000E-01 +PL 30.97400 2.44764E+00 2.15000E-01 1 1111111111 + 15 2.44764E+00 2.15000E-01 +DUM 0.00000 0.00000E+00 0.00000E+00 1 1111111111 + 0 0.00000E+00 0.00000E+00 +SOD 22.98977 1.96230E-01 1.36375E-01 1 1111111111 + 11 1.96230E-01 1.36375E-01 +POT 39.10200 3.64008E-01 1.76375E-01 1 1111111111 + 19 3.64008E-01 1.76375E-01 +CLA 35.45000 6.27600E-01 2.27000E-01 1 1111111111 + 17 6.27600E-01 2.27000E-01 +CAL 40.08000 5.02080E-01 1.36700E-01 1 1111111111 + 20 5.02080E-01 1.36700E-01 +MG 24.30500 6.27600E-02 1.18500E-01 1 1111111111 + 12 6.27600E-02 1.18500E-01 +CES 132.90000 7.94960E-01 2.10000E-01 1 1111111111 + 55 7.94960E-01 2.10000E-01 +ZN 65.37000 1.04600E+00 1.09000E-01 1 1111111111 + 30 1.04600E+00 1.09000E-01 +Cross +Bonds +CTL3 -CL 0.15220 1.67360E+05 +CTL2 -CL 0.15220 1.67360E+05 +CTL1 -CL 0.15220 1.67360E+05 +CTL1 -CCL 0.15220 1.67360E+05 +OBL -CL 0.12200 6.27600E+05 +OCL -CL 0.12600 4.39320E+05 +OCL -CCL 0.12600 4.39320E+05 +OSL -CL 0.13340 1.25520E+05 +OHL -CL 0.14000 1.92464E+05 +HOL -OHL 0.09600 4.56056E+05 +CTL1 -HAL1 0.11110 2.58571E+05 +CTL1 -HBL 0.10800 2.76144E+05 +CTL2 -HAL2 0.11110 2.58571E+05 +CTL3 -HAL3 0.11110 2.69450E+05 +CTL3 -OSL 0.14300 2.84512E+05 +CTL2 -OSL 0.14300 2.84512E+05 +CTL1 -OSL 0.14300 2.84512E+05 +OSL -PL 0.16000 2.25936E+05 +O2L -PL 0.14800 4.85344E+05 +OHL -PL 0.15900 1.98322E+05 +NH3L -HCL 0.10400 3.43088E+05 +NH3L -CTL1 0.14800 1.67360E+05 +NH3L -CTL2 0.15100 2.18405E+05 +NTL -CTL2 0.15100 1.79912E+05 +NTL -CTL5 0.15100 1.79912E+05 +CTL5 -HL 0.10800 2.51040E+05 +CTL2 -HL 0.10800 2.51040E+05 +CTL1 -CTL1 0.15000 1.86188E+05 +CTL1 -CTL2 0.15380 1.86188E+05 +CTL1 -CTL3 0.15380 1.86188E+05 +CTL2 -CTL2 0.15300 1.86188E+05 +CTL2 -CTL3 0.15280 1.86188E+05 +CTL3 -CTL3 0.15300 1.86188E+05 +OHL -CTL1 0.14200 3.58150E+05 +OHL -CTL2 0.14200 3.58150E+05 +OHL -CTL3 0.14200 3.58150E+05 +SL -O2L 0.14480 4.51872E+05 +SL -OSL 0.15750 2.09200E+05 +HT -HT 0.15139 0.00000E+00 +HT -OT 0.09572 3.76560E+05 +CEL2 -CEL2 0.13300 4.26768E+05 +HEL2 -CEL2 0.11000 3.05432E+05 +CEL1 -CTL3 0.15040 3.20494E+05 +CEL1 -CEL2 0.13420 4.18400E+05 +HEL1 -CEL1 0.11000 3.01666E+05 +CEL1 -CTL2 0.15020 3.05432E+05 +CEL1 -CEL1 0.13400 3.68192E+05 +Angles +OBL -CL -CTL3 2.18166 5.85760E+02 0.24420 1.67360E+02 +OBL -CL -CTL2 2.18166 5.85760E+02 0.24420 1.67360E+02 +OBL -CL -CTL1 2.18166 5.85760E+02 0.24420 1.67360E+02 +OSL -CL -OBL 2.19737 7.53120E+02 0.22576 1.33888E+03 +CL -OSL -CTL1 1.91288 3.34720E+02 0.22651 2.51040E+02 +CL -OSL -CTL2 1.91288 3.34720E+02 0.22651 2.51040E+02 +CL -OSL -CTL3 1.91288 3.34720E+02 0.22651 2.51040E+02 +HAL2 -CTL2 -CL 1.91114 2.76144E+02 0.21630 2.51040E+02 +HAL3 -CTL3 -CL 1.91114 2.76144E+02 0.21630 2.51040E+02 +CTL2 -CTL1 -CCL 1.88496 4.35136E+02 0.00000 0.00000E+00 +CTL2 -CTL2 -CL 1.88496 4.35136E+02 0.00000 0.00000E+00 +CTL3 -CTL2 -CL 1.88496 4.35136E+02 0.00000 0.00000E+00 +OSL -CL -CTL3 1.90241 4.60240E+02 0.23260 1.67360E+02 +OSL -CL -CTL2 1.90241 4.60240E+02 0.23260 1.67360E+02 +OSL -CL -CTL1 1.90241 4.60240E+02 0.23260 1.67360E+02 +OHL -CL -OBL 2.14675 4.18400E+02 0.22620 1.75728E+03 +OCL -CCL -CTL1 2.05949 3.34720E+02 0.23880 4.18400E+02 +OCL -CL -CTL2 2.05949 3.34720E+02 0.23880 4.18400E+02 +OCL -CL -CTL3 2.05949 3.34720E+02 0.23880 4.18400E+02 +OCL -CL -OCL 2.16421 8.36800E+02 0.22250 5.85760E+02 +OCL -CCL -OCL 2.16421 8.36800E+02 0.22250 5.85760E+02 +OHL -CL -CTL3 1.92859 4.60240E+02 0.00000 0.00000E+00 +OHL -CL -CTL2 1.92859 4.60240E+02 0.00000 0.00000E+00 +HOL -OHL -CL 2.00713 4.60240E+02 0.00000 0.00000E+00 +OSL -CTL1 -CTL2 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL1 -CTL3 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL2 -CTL1 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL2 -CTL2 1.92161 6.33458E+02 0.00000 0.00000E+00 +OSL -CTL2 -CTL3 1.92161 6.33458E+02 0.00000 0.00000E+00 +HAL2 -CTL2 -HAL2 1.90241 2.97064E+02 0.18020 4.51872E+01 +HAL3 -CTL3 -HAL3 1.89194 2.97064E+02 0.18020 4.51872E+01 +HAL1 -CTL1 -OSL 1.91114 5.02080E+02 0.00000 0.00000E+00 +HAL2 -CTL2 -OSL 1.91114 5.02080E+02 0.00000 0.00000E+00 +HAL3 -CTL3 -OSL 1.91114 5.02080E+02 0.00000 0.00000E+00 +CTL2 -OSL -PL 2.09440 1.67360E+02 0.23300 2.92880E+02 +CTL3 -OSL -PL 2.09440 1.67360E+02 0.23300 2.92880E+02 +HOL -OHL -PL 2.00713 2.51040E+02 0.23000 3.34720E+02 +OSL -PL -OSL 1.82038 6.69440E+02 0.00000 0.00000E+00 +OSL -PL -O2L 1.94779 8.27595E+02 0.00000 0.00000E+00 +OSL -PL -OHL 1.88496 4.02501E+02 0.00000 0.00000E+00 +O2L -PL -O2L 2.09440 1.00416E+03 0.00000 0.00000E+00 +O2L -PL -OHL 1.88897 8.27595E+02 0.00000 0.00000E+00 +NTL -CTL2 -HL 1.91114 3.34720E+02 0.21300 2.25936E+02 +NTL -CTL5 -HL 1.91114 3.34720E+02 0.21300 2.25936E+02 +HL -CTL2 -HL 1.91114 2.00832E+02 0.17670 2.34304E+02 +HL -CTL5 -HL 1.91114 2.00832E+02 0.17670 2.34304E+02 +CTL2 -NTL -CTL2 1.91114 5.02080E+02 0.24660 2.17568E+02 +CTL5 -NTL -CTL2 1.91114 5.02080E+02 0.24660 2.17568E+02 +CTL5 -NTL -CTL5 1.91114 5.02080E+02 0.24660 2.17568E+02 +HL -CTL2 -CTL2 1.92161 2.79742E+02 0.21790 1.88531E+02 +HL -CTL2 -CTL3 1.92161 2.79742E+02 0.21790 1.88531E+02 +HBL -CTL1 -CCL 1.91114 4.18400E+02 0.00000 0.00000E+00 +HBL -CTL1 -CTL2 1.93732 2.92880E+02 0.00000 0.00000E+00 +HAL1 -CTL1 -CTL1 1.92161 2.88696E+02 0.21790 1.88531E+02 +HAL1 -CTL1 -CTL2 1.92161 2.88696E+02 0.21790 1.88531E+02 +HAL1 -CTL1 -CTL3 1.92161 2.88696E+02 0.21790 1.88531E+02 +HAL2 -CTL2 -CTL1 1.92161 2.21752E+02 0.21790 1.88531E+02 +HAL2 -CTL2 -CTL2 1.92161 2.21752E+02 0.21790 1.88531E+02 +HAL2 -CTL2 -CTL3 1.92161 2.89533E+02 0.21790 1.88531E+02 +HAL3 -CTL3 -CTL1 1.92161 2.79742E+02 0.21790 1.88531E+02 +HAL3 -CTL3 -CTL2 1.92161 2.89533E+02 0.21790 1.88531E+02 +HAL3 -CTL3 -CTL3 1.92161 3.13800E+02 0.21790 1.88531E+02 +NTL -CTL2 -CTL2 2.00713 5.66514E+02 0.00000 0.00000E+00 +NTL -CTL2 -CTL3 2.00713 5.66514E+02 0.00000 0.00000E+00 +HCL -NH3L -CTL1 1.91114 2.51040E+02 0.20740 1.67360E+02 +HCL -NH3L -CTL2 1.91114 2.76144E+02 0.20560 3.34720E+01 +HCL -NH3L -HCL 1.91114 3.43088E+02 0.00000 0.00000E+00 +NH3L -CTL1 -CCL 1.91986 3.65682E+02 0.00000 0.00000E+00 +NH3L -CTL1 -CTL2 1.91986 5.66514E+02 0.00000 0.00000E+00 +NH3L -CTL2 -CTL2 1.91986 5.66514E+02 0.00000 0.00000E+00 +NH3L -CTL1 -HBL 1.87623 4.30952E+02 0.00000 0.00000E+00 +NH3L -CTL2 -HAL2 1.87623 3.76560E+02 0.20836 2.92880E+02 +CTL1 -CTL1 -CTL1 1.93732 4.46433E+02 0.25610 6.69440E+01 +CTL1 -CTL1 -CTL2 1.98095 4.88273E+02 0.25610 9.33869E+01 +CTL1 -CTL1 -CTL3 1.89368 4.46433E+02 0.25610 6.69440E+01 +CTL1 -CTL2 -CTL1 1.98095 4.88273E+02 0.25610 9.33869E+01 +CTL1 -CTL2 -CTL2 1.98095 4.88273E+02 0.25610 9.33869E+01 +CTL1 -CTL2 -CTL3 1.98095 4.88273E+02 0.25610 9.33869E+01 +CTL2 -CTL1 -CTL2 1.98095 4.88273E+02 0.25610 9.33869E+01 +CTL2 -CTL1 -CTL3 1.98095 4.88273E+02 0.25610 9.33869E+01 +CTL2 -CTL2 -CTL2 1.98269 4.88273E+02 0.25610 9.33869E+01 +CTL2 -CTL2 -CTL3 2.00713 4.85344E+02 0.25610 6.69440E+01 +HOL -OHL -CTL1 1.85005 4.81160E+02 0.00000 0.00000E+00 +HOL -OHL -CTL2 1.85005 4.81160E+02 0.00000 0.00000E+00 +HOL -OHL -CTL3 1.85005 4.81160E+02 0.00000 0.00000E+00 +OHL -CTL1 -CTL2 1.92161 6.33458E+02 0.00000 0.00000E+00 +OHL -CTL2 -CTL1 1.92161 6.33458E+02 0.00000 0.00000E+00 +OHL -CTL2 -CTL2 1.92161 6.33458E+02 0.00000 0.00000E+00 +OHL -CTL2 -CTL3 1.92161 6.33458E+02 0.00000 0.00000E+00 +OHL -CTL1 -HAL1 1.90049 3.84091E+02 0.00000 0.00000E+00 +OHL -CTL2 -HAL2 1.90049 3.84091E+02 0.00000 0.00000E+00 +OHL -CTL3 -HAL3 1.90049 3.84091E+02 0.00000 0.00000E+00 +O2L -SL -O2L 1.91061 1.08784E+03 0.24500 2.92880E+02 +O2L -SL -OSL 1.71042 7.11280E+02 0.00000 0.00000E+00 +CTL2 -OSL -SL 1.90241 1.25520E+02 0.19000 2.25936E+02 +CTL3 -OSL -SL 1.90241 1.25520E+02 0.19000 2.25936E+02 +HT -OT -HT 1.82422 4.60240E+02 0.00000 0.00000E+00 +CEL1 -CEL1 -CTL2 2.15548 4.01664E+02 0.00000 0.00000E+00 +CEL1 -CEL1 -CTL3 2.15548 4.01664E+02 0.00000 0.00000E+00 +CEL2 -CEL1 -CTL2 2.19911 4.01664E+02 0.00000 0.00000E+00 +CEL2 -CEL1 -CTL3 2.18515 3.93296E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CEL1 2.08567 4.35136E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CEL2 2.05949 3.51456E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CTL2 2.02458 3.34720E+02 0.00000 0.00000E+00 +HEL1 -CEL1 -CTL3 2.04204 1.84096E+02 0.00000 0.00000E+00 +HEL2 -CEL2 -CEL1 2.10312 3.76560E+02 0.00000 0.00000E+00 +HEL2 -CEL2 -CEL2 2.10312 4.64424E+02 0.00000 0.00000E+00 +HEL2 -CEL2 -HEL2 2.07694 1.58992E+02 0.00000 0.00000E+00 +CEL1 -CTL2 -CTL2 1.95826 2.67776E+02 0.00000 0.00000E+00 +CEL1 -CTL2 -CTL3 1.95826 2.67776E+02 0.00000 0.00000E+00 +HAL2 -CTL2 -CEL1 1.94604 3.76560E+02 0.00000 0.00000E+00 +HAL3 -CTL3 -CEL1 1.94604 3.51456E+02 0.00000 0.00000E+00 +CEL1 -CTL2 -CEL1 1.98968 2.51040E+02 0.00000 0.00000E+00 +Proper dihedrals + -CTL1 -OHL - 0.00000 5.85760E-01 3 + -CTL2 -OHL - 0.00000 5.85760E-01 3 + -CTL3 -OHL - 0.00000 5.85760E-01 3 +OCL -CCL -CTL1 -NH3L 3.14159 1.33888E+01 2 +OBL -CL -CTL2 -HAL2 3.14159 0.00000E+00 6 +OBL -CL -CTL3 -HAL3 3.14159 0.00000E+00 6 +OSL -CL -CTL2 -HAL2 3.14159 0.00000E+00 6 +OSL -CL -CTL3 -HAL3 3.14159 0.00000E+00 6 +OBL -CL -OSL -CTL1 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL1 3.14159 1.61084E+01 2 +OBL -CL -OSL -CTL2 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL2 3.14159 1.61084E+01 2 +OBL -CL -OSL -CTL3 3.14159 4.03756E+00 -1 +OBL -CL -OSL -CTL3 3.14159 1.61084E+01 2 + -CL -OSL - 3.14159 8.57720E+00 2 + -CTL1 -CCL - 3.14159 2.09200E-01 6 + -CTL2 -CL - 3.14159 2.09200E-01 6 + -CTL3 -CL - 3.14159 2.09200E-01 6 + -CL -OHL - 3.14159 8.57720E+00 2 +HAL2 -CTL2 -CL -OHL 3.14159 0.00000E+00 6 +HAL3 -CTL3 -CL -OHL 3.14159 0.00000E+00 6 +OSL -PL -OSL -CTL2 3.14159 5.02080E+00 -1 +OSL -PL -OSL -CTL2 3.14159 4.18400E-01 -2 +OSL -PL -OSL -CTL2 3.14159 4.18400E-01 3 +O2L -PL -OSL -CTL2 0.00000 4.18400E-01 3 +OSL -PL -OSL -CTL3 3.14159 5.02080E+00 -1 +OSL -PL -OSL -CTL3 3.14159 4.18400E-01 -2 +OSL -PL -OSL -CTL3 3.14159 4.18400E-01 3 +O2L -PL -OSL -CTL3 0.00000 4.18400E-01 3 +OHL -PL -OSL -CTL2 0.00000 3.97480E+00 -2 +OHL -PL -OSL -CTL2 0.00000 2.09200E+00 3 +OHL -PL -OSL -CTL3 0.00000 3.97480E+00 -2 +OHL -PL -OSL -CTL3 0.00000 2.09200E+00 3 + -OHL -PL - 0.00000 1.25520E+00 3 + -CTL1 -OSL - 0.00000 0.00000E+00 3 + -CTL2 -OSL - 0.00000 0.00000E+00 3 + -CTL3 -OSL - 0.00000 0.00000E+00 3 +CTL3 -CTL2 -OSL -CL 3.14159 2.92880E+00 1 +CTL2 -CTL2 -OSL -CL 3.14159 2.92880E+00 1 +CTL3 -CTL1 -OSL -CL 3.14159 2.92880E+00 1 +CTL2 -CTL1 -OSL -CL 3.14159 2.92880E+00 1 +CTL1 -CTL2 -CL -OSL 3.14159-6.27600E-01 -1 +CTL1 -CTL2 -CL -OSL 3.14159 2.21752E+00 2 +CTL3 -CTL2 -CL -OSL 3.14159-6.27600E-01 -1 +CTL3 -CTL2 -CL -OSL 3.14159 2.21752E+00 2 +CTL3 -CTL1 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL3 -CTL1 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL3 -CTL1 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL3 -CTL1 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL1 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL2 -CTL1 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL2 -CTL1 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL2 -CTL1 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL3 -CTL2 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL3 -CTL2 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL3 -CTL2 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL3 -CTL2 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL2 -CTL2 -OSL 0.00000 2.34304E-01 -4 +CTL2 -CTL2 -CTL2 -OSL 3.14159 5.48104E-01 -3 +CTL2 -CTL2 -CTL2 -OSL 0.00000 1.05018E+00 -2 +CTL2 -CTL2 -CTL2 -OSL 3.14159 9.28848E-01 1 +CTL2 -CTL2 -CL -OSL 0.00000 2.51040E-01 -4 +CTL2 -CTL2 -CL -OSL 3.14159 4.43504E-01 -3 +CTL2 -CTL2 -CL -OSL 3.14159 1.83678E+00 -2 +CTL2 -CTL2 -CL -OSL 0.00000 6.40152E-01 1 +CTL2 -CTL2 -CL -OBL 3.14159 8.36800E-02 -4 +CTL2 -CTL2 -CL -OBL 3.14159 1.04600E-01 2 +CTL3 -CTL2 -CTL2 -CL 0.00000 4.10032E-01 -4 +CTL3 -CTL2 -CTL2 -CL 3.14159 1.28449E+00 -3 +CTL3 -CTL2 -CTL2 -CL 0.00000 2.76981E+00 -2 +CTL3 -CTL2 -CTL2 -CL 0.00000 2.17150E+00 1 +CTL2 -CTL2 -CTL2 -CL 0.00000 4.10032E-01 -4 +CTL2 -CTL2 -CTL2 -CL 3.14159 1.28449E+00 -3 +CTL2 -CTL2 -CTL2 -CL 0.00000 2.76981E+00 -2 +CTL2 -CTL2 -CTL2 -CL 0.00000 2.17150E+00 1 + -CTL2 -NTL - 0.00000 1.08784E+00 3 + -CTL5 -NTL - 0.00000 9.62320E-01 3 + -CTL1 -NH3L - 0.00000 4.18400E-01 3 + -CTL2 -NH3L - 0.00000 4.18400E-01 3 +NH3L -CTL2 -CTL2 -OHL 3.14159 2.92880E+00 1 +NH3L -CTL2 -CTL2 -OSL 3.14159 2.92880E+00 1 +NTL -CTL2 -CTL2 -OHL 3.14159 1.79912E+01 -1 +NTL -CTL2 -CTL2 -OHL 3.14159-1.67360E+00 3 +NTL -CTL2 -CTL2 -OSL 3.14159 1.38072E+01 -1 +NTL -CTL2 -CTL2 -OSL 3.14159-1.67360E+00 3 + -CTL1 -CTL1 - 0.00000 8.36800E-01 3 + -CTL1 -CTL2 - 0.00000 8.36800E-01 3 + -CTL1 -CTL3 - 0.00000 8.36800E-01 3 + -CTL2 -CTL2 - 0.00000 7.94960E-01 3 + -CTL2 -CTL3 - 0.00000 6.69440E-01 3 + -CTL3 -CTL3 - 0.00000 6.38060E-01 3 +CTL3 -CTL2 -CTL2 -CTL3 0.00000 1.59787E-01 -2 +CTL3 -CTL2 -CTL2 -CTL3 3.14159 1.32968E-01 6 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 6.29734E-01 -2 +CTL2 -CTL2 -CTL2 -CTL3 3.14159 3.40285E-01 -3 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 4.52876E-01 -4 +CTL2 -CTL2 -CTL2 -CTL3 0.00000 8.53159E-01 5 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 2.69868E-01 -2 +CTL2 -CTL2 -CTL2 -CTL2 3.14159 6.26554E-01 -3 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 3.95723E-01 -4 +CTL2 -CTL2 -CTL2 -CTL2 0.00000 4.70742E-01 5 +HAL3 -CTL3 -OSL -SL 0.00000 0.00000E+00 3 +CTL2 -OSL -SL -O2L 0.00000 0.00000E+00 3 +CTL3 -OSL -SL -O2L 0.00000 0.00000E+00 3 +HEL1 -CEL1 -CEL1 -HEL1 3.14159 4.18400E+00 2 +CTL3 -CEL1 -CEL1 -HEL1 3.14159 4.18400E+00 2 + -CEL1 -CEL1 - 3.14159 1.88280E+00 -1 + -CEL1 -CEL1 - 3.14159 3.55640E+01 2 + -CEL2 -CEL2 - 3.14159 2.05016E+01 2 +CTL2 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +CTL3 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +HEL1 -CEL1 -CEL2 -HEL2 3.14159 2.17568E+01 2 +CEL1 -CEL1 -CTL2 -HAL2 3.14159 1.25520E+00 3 +CEL1 -CEL1 -CTL3 -HAL3 3.14159 1.25520E+00 3 +CEL1 -CEL1 -CTL2 -CTL3 3.14159 3.76560E+00 -1 +CEL1 -CEL1 -CTL2 -CTL3 3.14159 8.36800E-01 2 +CEL1 -CEL1 -CTL2 -CTL2 3.14159 2.51040E+00 1 +CEL1 -CTL2 -CTL2 -CTL3 1.57080 1.25520E+00 -1 +CEL1 -CTL2 -CTL2 -CTL3 0.00000 8.36800E-01 -2 +CEL1 -CTL2 -CTL2 -CTL3 3.14159 1.04600E+00 3 +CEL1 -CTL2 -CTL2 -CTL2 1.57080 1.25520E+00 -1 +CEL1 -CTL2 -CTL2 -CTL2 0.00000 8.36800E-01 -2 +CEL1 -CTL2 -CTL2 -CTL2 3.14159 1.04600E+00 3 +CEL2 -CEL1 -CTL2 -CTL2 3.14159 2.09200E+00 -1 +CEL2 -CEL1 -CTL2 -CTL2 3.14159 5.43920E+00 3 +CEL2 -CEL1 -CTL2 -CTL3 3.14159 2.09200E+00 -1 +CEL2 -CEL1 -CTL2 -CTL3 3.14159 5.43920E+00 3 +CEL2 -CEL1 -CTL2 -HAL2 0.00000 5.02080E-01 3 +CEL2 -CEL1 -CTL3 -HAL3 3.14159 2.09200E-01 3 +HEL1 -CEL1 -CTL2 -CTL2 0.00000 5.02080E-01 3 +HEL1 -CEL1 -CTL2 -CTL3 0.00000 5.02080E-01 3 +HEL1 -CEL1 -CTL2 -HAL2 0.00000 0.00000E+00 3 +HEL1 -CEL1 -CTL3 -HAL3 0.00000 0.00000E+00 3 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 5.02080E+00 -1 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 1.67360E+00 -2 +CEL2 -CEL1 -CTL2 -CEL1 3.14159 5.43920E+00 3 +CEL1 -CTL2 -CEL1 -HEL1 0.00000 0.00000E+00 -2 +CEL1 -CTL2 -CEL1 -HEL1 0.00000 0.00000E+00 3 +CEL1 -CEL1 -CTL2 -CEL1 3.14159 4.18400E+00 -1 +CEL1 -CEL1 -CTL2 -CEL1 0.00000 4.18400E-01 -2 +CEL1 -CEL1 -CTL2 -CEL1 3.14159 1.25520E+00 -3 +CEL1 -CEL1 -CTL2 -CEL1 0.00000 8.36800E-01 4 +Improper dihedrals +OBL - - -CL 0.00000 8.36800E+02 +HEL2 -HEL2 -CEL2 -CEL2 0.00000 2.51040E+01 +OCL - - -CL 0.00000 8.03328E+02 +OCL - - -CCL 0.00000 8.03328E+02 diff --git a/src/data/charmm_s/par_all35_ethers.par b/src/data/charmm_s/par_all35_ethers.par new file mode 100644 index 0000000..60fabed --- /dev/null +++ b/src/data/charmm_s/par_all35_ethers.par @@ -0,0 +1,232 @@ +CHARMM32 ether force field December 2006 file for ARGOS 7.0 +Electrostatic 1-4 scaling factor 1.000000 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +HCA1 1.00800 1.88280E-01 1.34000E-01 1 1111111111 + 1 1.88280E-01 1.34000E-01 +HCA2 1.00800 1.46440E-01 1.34000E-01 1 1111111111 + 1 1.46440E-01 1.34000E-01 +HCA3 1.00800 1.00416E-01 1.34000E-01 1 1111111111 + 1 1.00416E-01 1.34000E-01 +HT 1.00800 1.92464E-01 2.24500E-02 1 1111111111 + 1 1.92464E-01 2.24500E-02 +CC30A 12.01100 1.33888E-01 2.00000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CC31A 12.01100 1.33888E-01 2.00000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CC32A 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CC33A 12.01100 3.26352E-01 2.04000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CC326 12.01100 2.34304E-01 2.01000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +HCA25 1.00800 1.46440E-01 1.30000E-01 1 1111111111 + 1 1.46440E-01 1.30000E-01 +CC325 12.01100 2.51040E-01 2.02000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +CC325 12.01100 2.51040E-01 2.02000E-01 1 1111111111 + 6 4.18400E-02 1.90000E-01 +OC305 15.99900 4.18400E-01 1.65000E-01 1 1111111111 + 8 4.18400E-01 1.65000E-01 +OC30A 15.99900 4.18400E-01 1.65000E-01 1 1111111111 + 8 4.18400E-01 1.65000E-01 +OT 15.99900 6.36386E-01 1.76820E-01 1 1111111111 + 8 6.36386E-01 1.76820E-01 +HE 4.00260 8.89937E-02 1.48000E-01 1 1111111111 + 2 8.89937E-02 1.48000E-01 +NE 20.17970 3.59824E-01 1.53000E-01 1 1111111111 + 10 3.59824E-01 1.53000E-01 +DUM 0.00000 0.00000E+00 0.00000E+00 1 1111111111 + 0 0.00000E+00 0.00000E+00 +Cross +Bonds +CC31 -HCA1 0.11110 2.58571E+05 +CC32 -HCA2 0.11110 2.58571E+05 +CC33 -HCA3 0.11110 2.69450E+05 +CC30 -CC32 0.15380 1.86188E+05 +CC30 -CC33 0.15380 1.86188E+05 +CC31 -CC31 0.15000 1.86188E+05 +CC31 -CC32 0.15380 1.86188E+05 +CC31 -CC33 0.15380 1.86188E+05 +CC32 -CC32 0.15300 1.86188E+05 +CC32 -CC33 0.15280 1.86188E+05 +CC33 -CC33 0.15300 1.86188E+05 +CC32 -CC32 0.15480 1.63176E+05 +CC32 -HCA2 0.11160 2.56898E+05 +CC32 -OC30 0.14250 2.92880E+05 +CC32 -CC32 0.15180 1.63176E+05 +CC32 -HCA2 0.11000 2.56898E+05 +CC32 -CC33 0.15280 1.86188E+05 +CC32 -OC30 0.14150 3.01248E+05 +CC33 -OC30 0.14150 3.01248E+05 +CC32 -HCA2 0.11110 2.58571E+05 +CC32 -CC32 0.15300 1.86188E+05 +CC32 -OC30 0.14150 3.01248E+05 +HT -HT 0.15139 0.00000E+00 +OT -HT 0.09572 3.76560E+05 +Angles +HCA1 -CC31 -CC31 1.92161 2.88696E+02 0.21790 1.88531E+02 +HCA1 -CC31 -CC32 1.92161 2.88696E+02 0.21790 1.88531E+02 +HCA1 -CC31 -CC33 1.92161 2.88696E+02 0.21790 1.88531E+02 +HCA2 -CC32 -CC30 1.92161 2.21752E+02 0.21790 1.88531E+02 +HCA2 -CC32 -CC31 1.92161 2.21752E+02 0.21790 1.88531E+02 +HCA2 -CC32 -CC32 1.92161 2.21752E+02 0.21790 1.88531E+02 +HCA2 -CC32 -CC33 1.92161 2.89533E+02 0.21790 1.88531E+02 +HCA3 -CC33 -CC30 1.92161 2.79742E+02 0.21790 1.88531E+02 +HCA3 -CC33 -CC31 1.92161 2.79742E+02 0.21790 1.88531E+02 +HCA3 -CC33 -CC32 1.92161 2.89533E+02 0.21790 1.88531E+02 +HCA3 -CC33 -CC33 1.92161 3.13800E+02 0.21790 1.88531E+02 +HCA2 -CC32 -HCA2 1.90241 2.97064E+02 0.18020 4.51872E+01 +HCA3 -CC33 -HCA3 1.89194 2.97064E+02 0.18020 4.51872E+01 +CC30 -CC32 -CC32 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC30 -CC32 -CC33 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC31 -CC31 -CC31 1.93732 4.46433E+02 0.25610 6.69440E+01 +CC31 -CC31 -CC32 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC31 -CC31 -CC33 1.89368 4.46433E+02 0.25610 6.69440E+01 +CC31 -CC32 -CC31 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC31 -CC32 -CC32 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC31 -CC32 -CC33 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC32 -CC30 -CC32 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC32 -CC31 -CC32 1.98095 4.88273E+02 0.25610 9.33869E+01 +CC32 -CC32 -CC32 1.98269 4.88273E+02 0.25610 9.33869E+01 +CC32 -CC32 -CC33 2.00713 4.85344E+02 0.25610 6.69440E+01 +CC33 -CC30 -CC33 1.98968 4.46433E+02 0.25610 6.69440E+01 +CC33 -CC31 -CC32 1.98968 4.46433E+02 0.25610 6.69440E+01 +CC33 -CC31 -CC33 1.98968 4.46433E+02 0.25610 6.69440E+01 +CC33 -CC32 -CC33 1.98968 4.46433E+02 0.25610 6.69440E+01 +CC32 -CC32 -CC32 1.85005 4.85344E+02 0.25610 9.33869E+01 +HCA2 -CC32 -CC32 1.94430 2.92880E+02 0.21790 1.88531E+02 +HCA2 -CC32 -HCA2 1.86401 3.22168E+02 0.18020 4.51872E+01 +HCA2 -CC32 -CC32 1.94430 2.92880E+02 0.21790 1.88531E+02 +HCA2 -CC32 -HCA2 1.86401 3.22168E+02 0.18020 4.51872E+01 +CC32 -CC32 -CC32 1.91114 4.85344E+02 0.25610 9.33869E+01 +OC30 -CC32 -CC32 1.93906 3.76560E+02 0.00000 0.00000E+00 +CC32 -OC30 -CC32 1.93732 7.94960E+02 0.00000 0.00000E+00 +HCA2 -CC32 -OC30 1.87274 5.85760E+02 0.00000 0.00000E+00 +HCA3 -CC33 -CC32 1.92161 2.89533E+02 0.21790 1.88531E+02 +CC32 -CC32 -CC33 2.00713 4.85344E+02 0.25610 6.69440E+01 +HCA2 -CC32 -CC33 1.92161 2.89533E+02 0.21790 1.88531E+02 +OC30 -CC32 -CC33 1.94604 3.76560E+02 0.00000 0.00000E+00 +CC32 -OC30 -CC32 1.91463 7.94960E+02 0.00000 0.00000E+00 +CC33 -OC30 -CC32 1.91463 7.94960E+02 0.00000 0.00000E+00 +CC33 -OC30 -CC33 1.91463 7.94960E+02 0.00000 0.00000E+00 +OC30 -CC32 -CC32 1.94604 3.76560E+02 0.00000 0.00000E+00 +OC30 -CC32 -CC33 1.94604 3.76560E+02 0.00000 0.00000E+00 +HCA3 -CC33 -OC30 1.91114 5.02080E+02 0.00000 0.00000E+00 +HCA2 -CC32 -OC30 1.91114 5.02080E+02 0.00000 0.00000E+00 +HCA2 -CC32 -CC32 1.92161 2.88696E+02 0.21790 1.88531E+02 +HCA2 -CC32 -HCA2 1.90241 2.97064E+02 0.18020 4.51872E+01 +CC32 -CC32 -CC32 1.95477 4.88273E+02 0.25610 9.33869E+01 +OC30 -CC32 -CC32 1.94604 3.76560E+02 0.00000 0.00000E+00 +CC32 -OC30 -CC32 1.91463 7.94960E+02 0.00000 0.00000E+00 +HCA2 -CC32 -OC30 1.91114 3.76560E+02 0.00000 0.00000E+00 +HT -OT -HT 1.82422 4.60240E+02 0.00000 0.00000E+00 +Proper dihedrals +CC31 -CC30 -CC32 -HCA2 0.00000 8.36800E-01 3 +CC32 -CC30 -CC32 -HCA2 0.00000 8.36800E-01 3 +CC33 -CC30 -CC32 -HCA2 0.00000 8.36800E-01 3 +CC31 -CC30 -CC33 -HCA3 0.00000 8.36800E-01 3 +CC32 -CC30 -CC32 -HCA3 0.00000 8.36800E-01 3 +CC33 -CC30 -CC32 -HCA3 0.00000 8.36800E-01 3 +HCA1 -CC31 -CC31 -HCA1 0.00000 8.36800E-01 3 +CC31 -CC31 -CC31 -HCA1 0.00000 8.36800E-01 3 +CC32 -CC31 -CC31 -HCA1 0.00000 8.36800E-01 3 +CC33 -CC31 -CC31 -HCA1 0.00000 8.36800E-01 3 +HCA1 -CC31 -CC32 -HCA2 0.00000 8.36800E-01 3 +HCA1 -CC31 -CC32 -CC31 0.00000 8.36800E-01 3 +HCA1 -CC31 -CC32 -CC32 0.00000 8.36800E-01 3 +HCA1 -CC31 -CC32 -CC33 0.00000 8.36800E-01 3 +CC31 -CC31 -CC32 -HCA2 0.00000 8.36800E-01 3 +CC32 -CC31 -CC32 -HCA2 0.00000 8.36800E-01 3 +CC33 -CC31 -CC32 -HCA2 0.00000 8.36800E-01 3 +HCA1 -CC31 -CC33 -HCA3 0.00000 8.36800E-01 3 +CC31 -CC31 -CC33 -HCA3 0.00000 8.36800E-01 3 +CC32 -CC31 -CC33 -HCA3 0.00000 8.36800E-01 3 +CC33 -CC31 -CC33 -HCA3 0.00000 8.36800E-01 3 +HCA2 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +CC30 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +CC31 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +CC32 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +CC33 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +HCA2 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC30 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC31 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC32 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC33 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC33 -CC32 -CC32 -CC33 3.14159 1.33009E-01 -6 +CC33 -CC32 -CC32 -CC33 0.00000 1.59787E-01 2 +CC33 -CC32 -CC32 -CC32 0.00000 8.53159E-01 -5 +CC33 -CC32 -CC32 -CC32 0.00000 4.52876E-01 -4 +CC33 -CC32 -CC32 -CC32 3.14159 3.40285E-01 -3 +CC33 -CC32 -CC32 -CC32 0.00000 6.29734E-01 2 +CC32 -CC32 -CC32 -CC32 0.00000 4.70742E-01 -5 +CC32 -CC32 -CC32 -CC32 0.00000 3.95723E-01 -4 +CC32 -CC32 -CC32 -CC32 3.14159 6.26554E-01 -3 +CC32 -CC32 -CC32 -CC32 0.00000 2.69868E-01 2 +CC33 -CC32 -CC32 -CC33 0.00000 6.69440E-01 3 +CC33 -CC32 -CC32 -CC32 0.00000 6.69440E-01 3 +CC33 -CC32 -CC32 -HCA2 0.00000 6.69440E-01 3 +HCA2 -CC32 -CC32 -HCA2 0.00000 6.69440E-01 3 +CC32 -CC32 -CC32 -HCA2 0.00000 6.69440E-01 3 +CC32 -CC32 -CC32 -CC32 3.14159 1.71544E+00 3 +CC33 -CC32 -CC32 -CC33 0.00000 7.94960E-01 3 +CC33 -CC32 -CC32 -CC32 0.00000 7.94960E-01 3 +CC33 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +HCA2 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +CC32 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +OC30 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +HCA2 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC32 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +OC30 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC32 -CC32 -CC32 -CC32 3.14159 1.71544E+00 3 +HCA2 -CC32 -OC30 -CC32 0.00000 1.25520E+00 3 +OC30 -CC32 -CC32 -CC32 0.00000 0.00000E+00 3 +CC32 -CC32 -OC30 -CC32 0.00000 2.09200E+00 3 +CC33 -CC32 -OC30 -CC32 0.00000 1.25520E+00 3 +CC33 -CC32 -CC32 -CC33 0.00000 7.94960E-01 3 +CC33 -CC32 -CC32 -CC32 0.00000 7.94960E-01 3 +CC33 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +HCA2 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +HCA2 -CC32 -CC32 -CC32 0.00000 7.94960E-01 3 +OC30 -CC32 -CC32 -HCA2 0.00000 7.94960E-01 3 +HCA2 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC32 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +OC30 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +CC32 -CC32 -CC32 -CC32 0.00000 2.08485E+00 -2 +CC32 -CC32 -CC32 -CC32 0.00000-2.50387E+00 -3 +CC32 -CC32 -CC32 -CC32 0.00000 1.74665E+00 -4 +CC32 -CC32 -CC32 -CC32 0.00000-1.03885E+00 5 +OC30 -CC32 -CC32 -CC32 0.00000-8.04374E-01 -1 +OC30 -CC32 -CC32 -CC32 0.00000-4.18400E+00 -2 +OC30 -CC32 -CC32 -CC32 0.00000 2.48768E+00 -3 +OC30 -CC32 -CC32 -CC32 0.00000-3.28946E-01 4 +HCA3 -CC33 -CC33 -HCA3 0.00000 6.38060E-01 3 +CC32 -OC30 -CC32 -CC32 0.00000-2.20505E+00 -1 +CC32 -OC30 -CC32 -CC32 0.00000 2.85755E+00 -2 +CC32 -OC30 -CC32 -CC32 0.00000-8.77678E-01 -3 +CC32 -OC30 -CC32 -CC32 0.00000 6.29148E-01 4 +CC32 -OC30 -CC32 -HCA2 0.00000 1.18826E+00 3 +HCA2 -CC32 -CC32 -OC30 0.00000 7.94960E-01 3 +OC30 -CC32 -CC33 -HCA3 0.00000 6.69440E-01 3 +HCA2 -CC32 -OC30 -CC32 0.00000 1.18826E+00 3 +HCA3 -CC33 -OC30 -CC32 0.00000 1.18826E+00 3 +HCA2 -CC32 -OC30 -CC33 0.00000 1.18826E+00 3 +HCA3 -CC33 -OC30 -CC33 0.00000 1.18826E+00 3 +CC33 -CC32 -OC30 -CC32 0.00000 1.67360E+00 -1 +CC33 -CC32 -OC30 -CC32 0.00000 2.05016E+00 3 +CC33 -CC32 -OC30 -CC33 0.00000 1.67360E+00 -1 +CC33 -CC32 -OC30 -CC33 0.00000 2.05016E+00 3 +CC32 -CC32 -OC30 -CC33 0.00000 2.38488E+00 -1 +CC32 -CC32 -OC30 -CC33 0.00000 1.21336E+00 -2 +CC32 -CC32 -OC30 -CC33 0.00000 1.79912E+00 3 +CC32 -CC32 -OC30 -CC32 0.00000 2.38488E+00 -1 +CC32 -CC32 -OC30 -CC32 0.00000 1.21336E+00 -2 +CC32 -CC32 -OC30 -CC32 0.00000 1.79912E+00 3 +OC30 -CC32 -CC32 -OC30 3.14159 2.46856E+00 -1 +OC30 -CC32 -CC32 -OC30 0.00000 4.85344E+00 2 +OC30 -CC32 -CC32 -CC33 3.14159 6.69440E-01 -1 +OC30 -CC32 -CC32 -CC33 0.00000 1.63176E+00 2 +OC30 -CC32 -CC32 -CC32 3.14159 6.69440E-01 -1 +OC30 -CC32 -CC32 -CC32 0.00000 1.63176E+00 2 +Improper dihedrals diff --git a/src/data/charmm_x/GLU_C.frg b/src/data/charmm_x/GLU_C.frg new file mode 100644 index 0000000..a2d110e --- /dev/null +++ b/src/data/charmm_x/GLU_C.frg @@ -0,0 +1,38 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GLU_C + 16 1 1 0 +GLU_C + 1 N NH1 1 1 0 1 1 -0.179830 0.000000 + 2 H H 0 0 0 1 1 0.081563 0.000000 + 3 CA CT1 0 0 0 1 1 0.074962 0.000000 + 4 HA HB 0 0 0 1 1 0.041965 0.000000 + 5 CB CT2 0 0 0 1 1 0.026653 0.000000 + 62HB HA 0 0 0 1 1 -0.053970 0.000000 + 73HB HA 0 0 0 1 1 0.046859 0.000000 + 8 CG CT2 0 0 0 1 1 0.023370 0.000000 + 92HG HA 0 0 0 1 1 -0.035379 0.000000 + 103HG HA 0 0 0 1 1 -0.056946 0.000000 + 11 CD CC 0 1 0 1 1 0.095388 0.000000 + 12 OE1 OC 0 0 0 1 1 -0.526577 0.000000 + 13 OE2 OC 0 0 0 1 1 -0.515265 0.000000 + 14 C CC 0 1 0 1 1 0.036838 0.000000 + 15 O OC 0 0 0 1 1 -0.534769 0.000000 + 16 OXT OC 0 0 0 1 1 -0.524861 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 14 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 14 15 + 14 16 diff --git a/src/data/charmm_x/MET_N.frg b/src/data/charmm_x/MET_N.frg new file mode 100644 index 0000000..8235f8d --- /dev/null +++ b/src/data/charmm_x/MET_N.frg @@ -0,0 +1,44 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$MET_N + 19 1 1 0 +MET_N + 1 N NH3 0 0 0 1 1 0.114710 0.000000 + 22H HC 0 0 0 1 1 0.214756 0.000000 + 33H HC 0 0 0 1 1 0.199641 0.000000 + 44H HC 0 0 0 1 1 0.212340 0.000000 + 5 CA CT1 0 0 0 1 1 0.111169 0.000000 + 6 HA HB 0 0 0 1 1 0.021244 0.000000 + 7 CB CT2 0 0 0 1 1 0.003817 0.000000 + 82HB HA 0 0 0 1 1 0.007074 0.000000 + 93HB HA 0 0 0 1 1 0.051393 0.000000 + 10 CG CT2 0 0 0 1 1 -0.042239 0.000000 + 112HG HA 0 0 0 1 1 0.020552 0.000000 + 123HG HA 0 0 0 1 1 0.059976 0.000000 + 13 SD S 0 0 0 1 1 -0.112570 0.000000 + 14 CE CT3 0 0 0 1 1 -0.025640 0.000000 + 152HE HA 0 0 0 1 1 0.018357 0.000000 + 163HE HA 0 0 0 1 1 0.041025 0.000000 + 174HE HA 0 0 0 1 1 0.061081 0.000000 + 18 C C 2 1 0 1 1 0.266430 0.000000 + 19 O O 0 0 0 1 1 -0.223117 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 5 18 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 14 15 + 14 16 + 14 17 + 18 19 diff --git a/src/data/charmm_x/Na.frg b/src/data/charmm_x/Na.frg new file mode 100644 index 0000000..eded624 --- /dev/null +++ b/src/data/charmm_x/Na.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$Na + 1 1 1 0 +Na + 1Na Na 0 0 0 1 1 1.000000 0.000000 diff --git a/src/data/charmm_x/Na_M.frg b/src/data/charmm_x/Na_M.frg new file mode 100644 index 0000000..ff5b796 --- /dev/null +++ b/src/data/charmm_x/Na_M.frg @@ -0,0 +1,8 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$Na_M + 1 1 1 0 +Na_M + 1Na Na 0 0 0 1 1 1.000000 0.000000 diff --git a/src/data/charmm_x/spce.sgm b/src/data/charmm_x/spce.sgm new file mode 100644 index 0000000..ae37e49 --- /dev/null +++ b/src/data/charmm_x/spce.sgm @@ -0,0 +1,17 @@ +# +$spce + 4.600000 + 3 3 0 0 0 0 1 1 + 5.220000 + 1 OW 1 1 0 1 1 + OWS -0.847600 0.000000 + 22HW 0 0 0 1 1 + HWS 0.423800 0.000000 + 33HW 0 0 0 1 1 + HWS 0.423800 0.000000 + 1 1 2 1 1 + 0.100000 0.10000E+07 + 2 1 3 1 1 + 0.100000 0.10000E+07 + 3 2 3 1 1 + 0.163333 0.10000E+07 diff --git a/src/data/charmm_x/spce_M.sgm b/src/data/charmm_x/spce_M.sgm new file mode 100644 index 0000000..ae37e49 --- /dev/null +++ b/src/data/charmm_x/spce_M.sgm @@ -0,0 +1,17 @@ +# +$spce + 4.600000 + 3 3 0 0 0 0 1 1 + 5.220000 + 1 OW 1 1 0 1 1 + OWS -0.847600 0.000000 + 22HW 0 0 0 1 1 + HWS 0.423800 0.000000 + 33HW 0 0 0 1 1 + HWS 0.423800 0.000000 + 1 1 2 1 1 + 0.100000 0.10000E+07 + 2 1 3 1 1 + 0.100000 0.10000E+07 + 3 2 3 1 1 + 0.163333 0.10000E+07 diff --git a/src/data/solvents/clfm.rst b/src/data/solvents/clfm.rst new file mode 100644 index 0000000..2568dfd --- /dev/null +++ b/src/data/solvents/clfm.rst @@ -0,0 +1,1525 @@ +Restart file + + + 3.30000000/09/19 12:43:53 5 F + 1 0 + 3.319758 .000000 .000000 + .000000 3.319758 .000000 + .000000 .000000 2.644195 + 1.00922E+07 + 301.170328 301.170328 .000000 + 216 5 0 0 216 0 0 0 0 + .16699480 .91024657 -.04545994 -.48859675 -.41352415 -.52748780 + .20071265 .94820555 .05212194 .99946783 -1.44113738 -.60834644 + .25203623 .99666428 -.16817786 -.31703194 -.28686880 -.13864304 + .00136754 .95376064 -.05036688 -.43220340 -.35152764 .37693105 + .19281932 .73486503 -.06016052 .09619647 .01579789 .41961471 +0 1.62992621 4.56332587 3.80502886 + -.39333926 .21507745 .70005666 .50289158 .89146362 .23918799 + -.48350412 .16419399 .66289254 .97844954 -.29809928 .66507886 + -.29833801 .24971313 .55844218 .06715543 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+ 3 11 16 2473 + 4 13 15 2564 + 4 13 16 2649 + 4 14 15 2766 + 4 14 16 2855 From 02608cf25a502f6777f33583bf00a4752d0319f4 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Wed, 29 Nov 2023 23:29:08 -0800 Subject: [PATCH 06/11] Added some scf files --- src/ddscf/comp4_ext.c | 32 +++++++++ src/ddscf/fock_2e_file.c | 142 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 174 insertions(+) create mode 100644 src/ddscf/comp4_ext.c create mode 100644 src/ddscf/fock_2e_file.c diff --git a/src/ddscf/comp4_ext.c b/src/ddscf/comp4_ext.c new file mode 100644 index 0000000..b97284e --- /dev/null +++ b/src/ddscf/comp4_ext.c @@ -0,0 +1,32 @@ +#include +#include "bitops_decls.h" +#include "bitops_funcs.h" + +void comp4_extract(int* m, int i, double s, int nb_per_i) { + + int v; // Value after compression + +#if defined(CRAY) + int vv, vvv; +#endif + + int index, nbits; + double fast[] = {0.0, 1.0e-13, 1.0e-12, 1.0e-11, 1.0e-10, 1.0e-9, + 1.0e-8, 1.0e-7, 1.0e-6, 1.0e-5, 1.0e-4, 1.0e-3, 1.0e-2, + 1.0e-1, 1.0e0, 1.0e1}; + + v = 15; + index = (i - 1)/(2*nb_per_i) + 1; + nbits = 4*(i - (index-1)*(2*nb_per_i) - 1); +#if defined(CRAY) + vvv = shiftl(v, nbits); + vv = shiftr(iand(m(index), vvv), nbits); + v = iand(vv,15); +#else + v = iand(ishft(iand(m(index), ishft(v, nbits)), -nbits),15); +#endif + + s = fast(v); + // printf('%d -> %d %d %d %0.4f'); + +} diff --git a/src/ddscf/fock_2e_file.c b/src/ddscf/fock_2e_file.c new file mode 100644 index 0000000..fa0021c --- /dev/null +++ b/src/ddscf/fock_2e_file.c @@ -0,0 +1,142 @@ +#include "util.h" +#include "cscfps.h" +#include "cfock.h" +#include +#include + +void fock_2e_from_file(int geom, int basis, int nfock, int ablklen, + double jfac[nfock], double kfac[nfock], double tol2e, bool oskel, + double dij[nfock*ablklen], double dik[nfock*ablklen], double dli[nfock*ablklen], + double djk[nfock*ablklen], double dlj[nfock*ablklen], double dlk[nfock*ablklen], + double fij[nfock*ablklen], double fik[nfock*ablklen], double fli[nfock*ablklen], + double fjk[nfock*ablklen], double flj[nfock*ablklen], double flk[nfock*ablklen], + double tmp, int vg_dens[nfock], int vg_fock[nfock]) { + + //$Id$ + + /*Accumulate the contribution to the fock matrices from + integrals store in the integral file. Simply read thru + the file getting a range of indices, fetch the corresponding + density matrix blocks and then read the integrals in that + block. + */ + + double den_tol, denmax, dtol2e; + int ilo, jlo, klo, llo; + int ihi, jhi, khi, lhi; + int ijk_prev[3][2]; + int blklen; + + bool int2e_get_bf_range, int2e_file_read; + + if (oscfps) pstat_on(ps_fock_io); + + den_tol = fmax(tol2e*0.01, 1e-300); // To avoid a hard zero + + ijk_prev[0][0] = -1; + ijk_prev[1][0] = -1; + ijk_prev[2][0] = -1; + ijk_prev[0][1] = -1; + ijk_prev[1][1] = -1; + ijk_prev[2][1] = -1; + + blklen = nfock*ablklen; + dfill(blklen, 0.0e0, fij, 1); + dfill(blklen, 0.0e0, fik, 1); + dfill(blklen, 0.0e0, fli, 1); + dfill(blklen, 0.0e0, fjk, 1); + dfill(blklen, 0.0e0, flj, 1); + dfill(blklen, 0.0e0, flk, 1); + + // Loop over blocks of integral labels + + while (int2e_get_bf_range(ilo,ihi,jlo,jhi,klo,khi,llo,lhi)) { + // Get matrices for this block of labels + fock_init_cmul(ihi-ilo+1,jhi-jlo+1,lhi-llo+1); + fock_2e_cache_dens_fock( + ilo, jlo, klo, llo, + ihi, jhi, khi, lhi, + ijk_prev, + nfock, vg_dens, vg_fock, + jfac, kfac, + dij, dik, dli, djk, dlj, dlk, + fij, fik, fli, fjk, flj, flk, + tmp); + + fock_density_screen(nfock, + ilo, jlo, klo, llo, + ihi, jhi, khi, lhi, + ilo, jlo, klo, llo, + ihi, jhi, khi, lhi, + dij, dik, dli, djk, dlj, dlk, denmax) + + dtol2e = min(dentolmax, den_tol/max(1e-10,denmax), den_tol/max(1e-10,denmax**2)) + + call int2e_file_fock_block(nfock, dtol2e, + dij, dik, dli, djk, dlj, dlk, + fij, fik, fli, fjk, flj, flk) + + // Update F blocks + + call fock_upd_blk(nfock, vg_fock, + llo, lhi, ilo, ihi, kfac, fli, tmp) + call fock_upd_blk(nfock, vg_fock, + llo, lhi, jlo, jhi, kfac, flj, tmp) + call fock_upd_blk(nfock, vg_fock, + llo, lhi, klo, khi, jfac, flk, tmp) + } + + if (ijk_prev[0][0]) != -1) { + fock_upd_blk(nfock, vg_fock, + ijk_prev[0][0]), ijk_prev[0][1]), + ijk_prev(2,1), ijk_prev(2,2), + jfac, fij, tmp) + fock_upd_blk(nfock, vg_fock, + ijk_prev(2,1), ijk_prev(2,2), + ijk_prev(3,1), ijk_prev(3,2), + kfac, fjk, tmp ) + fock_upd_blk( nfock, vg_fock, + ijk_prev(1,1), ijk_prev(1,2), + ijk_prev(3,1), ijk_prev(3,2), + kfac, fik, tmp ) + } + + if (oscfps) pstat_off(ps_fock_io); + +} + +void fock_2e_rep_from_file(int geom, int basis, int nfock, int nbf, + double jfac[nfock], double kfac[nfock], double tol2e, bool oskel, + double dens[nfock][nbf*nbf], fock[nfock][nbf*nbf]) { + + double den_tol, denmax; + int ilo, jlo, klo, llo; + int ihi, jhi, khi, lhi, i, j; + + bool int2e_get_bf_range, int2e_file_read; + int idamax; + + if (oscfps) pstat_on(ps_fock_io); + + denmax = 0.0; + for (i = 0; i < nfock; i++) { + j = idamax(nbf*nbf, dens[i][0], nfock); + denmax = max(denmax, abs(dens[i][j]); + } + // return if DM is null (e.g imaginary part of RTTDFT DM at t=0) + if (denmax < 1e-12) return; + den_tol = min(dentolmax,tol2e/denmax,tol2e/denmax**2) // Threshold to screen integs only + + if (ga_nodeid() == 0 && util_print('fockfile',print_debug)) { + printf("fockfile: tols %d %d %d %d", tol2e, dentolmax, denmax, den_tol); + } + + fock_init_cmul(nbf,nbf,nbf) // lookup table for f build + + // Loop over blocks of integral labels +} + + + + +} From 8663962fcfc61105f6e52f268b69331532e91841 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Wed, 6 Dec 2023 02:37:36 -0800 Subject: [PATCH 07/11] Moved from C++ to C. Updated Python files. --- .gitignore | 7 +- src/basis/getlibr.py | 71 +++++++-- src/{nwchem.cpp => nwchem.c} | 6 +- src/rtdb/rtdb.h | 288 ++++++++++++++++++++++------------- src/tce/oce.py | 24 ++- src/tce/splitfiles.py | 17 +-- src/util/errquit.h | 6 +- 7 files changed, 270 insertions(+), 149 deletions(-) mode change 100644 => 100755 src/basis/getlibr.py rename src/{nwchem.cpp => nwchem.c} (99%) diff --git a/.gitignore b/.gitignore index 71319bc..0062803 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,8 @@ +.vscode +bin/ +build/ +include/ +lib/ ### C ### # Prerequisites @@ -19,7 +24,6 @@ *.gch *.pch - # Libraries *.dll *.so @@ -89,6 +93,7 @@ ehthumbs_vista.db # Folder config file Desktop.ini +.DS_Store # Recycle Bin used on file shares $RECYCLE.BIN/ diff --git a/src/basis/getlibr.py b/src/basis/getlibr.py old mode 100644 new mode 100755 index c5aefbf..e8ae321 --- a/src/basis/getlibr.py +++ b/src/basis/getlibr.py @@ -1,26 +1,35 @@ -#!/usr/bin/env python3 +#!/usr/bin/python3 # This script downloads the basis set library data from www.basissetexchange.org # into the directory $NWCHEM_TOP/src/basis/libraries.bse -# to use, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/ +# To run, cd $NWCHEM_TOP/src/basis/libraries.bse/ && ../getlibr.py +# this will update the content of $NWCHEM_TOP/src/basis/libraries.bse +# To use the updates library, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/ # Requires the installation of the python env. from # https://github.com/MolSSI-BSE/basis_set_exchange +# e.g. python3 -m pip install --user basis_set_exchange # See https://molssi-bse.github.io/basis_set_exchange/ # # names changed # def2-universal-jfit was weigend_coulomb_fitting # dgauss-a1-dftjfit was dgauss_a1_dft_coulomb_fitting # dgauss-a2-dftjfit was dgauss_a2_dft_coulomb_fitting -# + import basis_set_exchange as bse from datetime import datetime today = datetime.now().isoformat(timespec='minutes') print(today) all_bs = bse.get_all_basis_names() md = bse.get_metadata() -for bas_name in all_bs: - #get version and list of elements - version_bs = md[bas_name]['latest_version'] - elements_list = md[bas_name]['versions'][version_bs]['elements'] +summary_file = open('summary.txt','w') + +def writebs(md, bas_name, summary_file, get_aux=0): + md_bas_name = bas_name.lower() + md_bas_name = md_bas_name.replace("*","_st_") + md_bas_name = md_bas_name.replace("/","_sl_") + print(' md_bas_name '+md_bas_name+"\n") + print(' bas_name '+bas_name+"\n") + version_bs = md[md_bas_name]['latest_version'] + elements_list = md[md_bas_name]['versions'][version_bs]['elements'] #open file # get rid of asterisks file_name = bas_name.replace("*","s") @@ -33,19 +42,38 @@ for bas_name in all_bs: file_name = file_name.replace(" ","_") #replace forward slash with underscore file_name = file_name.replace("/","_") + #lowercase + file_name = file_name.lower() + if get_aux==1: + file_name = file_name + "-autoaux" print(' file name is '+file_name+"\n") output_file = open(file_name,'w') output_file.write('# BSE Version '+bse.version()+'\n') - output_file.write('# Data downloaded at '+today+'\n') - output_file.write('# '+bas_name+' version number '+version_bs+'\n') - output_file.write('# Description: '+md[bas_name]['description']+'\n') - output_file.write('# Role: '+md[bas_name]['role']+'\n') - output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# ')) - output_file.write('# \n') + output_file.write('# Data downloaded on '+today+'\n') + + if get_aux==0: + output_file.write('# '+bas_name+' version number '+version_bs+'\n') + output_file.write('# Description: '+md[md_bas_name]['description']+'\n') + output_file.write('# Role: '+md[md_bas_name]['role']+'\n') + output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# ')) + output_file.write('# \n') + elif get_aux==1: + output_file.write('# '+bas_name+' version number '+version_bs+' AutoAux \n') + output_file.write('# Role: JK Fitting \n') + output_file.write('# Stoychev GL, Auer AA, Neese F. \n# Automatic Generation of Auxiliary Basis Sets.\n# J Chem Theory Comput. 2017 Feb 14;13(2):554-562.\n# doi: 10.1021/acs.jctc.6b01041.\n') + output_file.write('# \n') + + n_elements=0 + for element in elements_list: + n_elements = n_elements + 1 + if get_aux==1: + summary_file.write('Basis set \"'+bas_name+'-autoaux\" (number of atoms '+str(n_elements)+')\n') + else: + summary_file.write('Basis set \"'+bas_name+'\" (number of atoms '+str(n_elements)+')\n') for element in elements_list: #element='h' try: - bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True) + bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True, get_aux=get_aux) except: # print("failed for"+element) pass @@ -54,11 +82,22 @@ for bas_name in all_bs: bs_str=bs_str.replace("END","end") bs_str=bs_str.replace("PRINT","") element_str=bse.misc.compact_elements([element]) - bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name) + if get_aux==1: + bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name+"-autoaux") + else: + bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name) #ECP bs_str=bs_str.replace("ECP","ecp \""+element_str+"_"+bas_name+"\"") output_file.write(bs_str) # print(bas_name+" "+element_str) -print("end") + return +for bas_name in all_bs: + md_bas_name = bas_name.lower() + md_bas_name = md_bas_name.replace("*","_st_") + md_bas_name = md_bas_name.replace("/","_sl_") + writebs(md, bas_name, summary_file) + if md[md_bas_name]['role'] == 'orbital': + writebs(md, bas_name, summary_file, get_aux=1) +print("end") \ No newline at end of file diff --git a/src/nwchem.cpp b/src/nwchem.c similarity index 99% rename from src/nwchem.cpp rename to src/nwchem.c index 620af57..e98437a 100644 --- a/src/nwchem.cpp +++ b/src/nwchem.c @@ -265,7 +265,7 @@ int main(){ errquit('start: rtdb_open old failed', 0, RTDB_ERR); } } - + // initialize nxtask nxtask_init(rtdb); @@ -344,7 +344,7 @@ int main(){ errquit('control: rtdb_print failed', 0, RTDB_ERR); } } - + if (!rtdb_close(rtdb, 'keep')){ errquit('nwchem: rtdb_close failed', rtdb, RTDB_ERR); } @@ -372,7 +372,7 @@ int main(){ ga_print_stats(); write(LuOut,*); } - + } diff --git a/src/rtdb/rtdb.h b/src/rtdb/rtdb.h index c50f473..069b115 100644 --- a/src/rtdb/rtdb.h +++ b/src/rtdb/rtdb.h @@ -1,105 +1,183 @@ -// -// Header file for intial FORTRAN interface to RTDB -// (see the C header file rtdb.h for more detail) -// -// All functions return .TRUE. on success, .FALSE. on failure -// -// All functions are also mirrored by routines rtdb_* -> rtdb_par_* -// in which process 0 performs the operation and all other processes -// are broadcast the result of a read and discard writes. -// -// rtdb_max_key ... an integer parameter that defines the maximum -// length of a character string key -// -// rtdb_max_file ... an integer parameter that defines the maximum -// length of a file name -// -// -// logical function rtdb_parallel(mode) -// logical mode [input] -// -// -// logical function rtdb_open(filename, mode, handle) -// character *(*) filename [input] -// character *(*) mode [input] -// integer handle [output] -// -// logical function rtdb_clone(handle, suffix) -// integer handle [input] -// character*(*) suffix [input] -// -// logical function rtdb_close(handle, mode) -// integer handle [input] -// character*(*) mode [input] -// -// logical function rtdb_put(handle, name, ma_type, nelem, array) -// integer handle [input] -// character *(*) name [input] -// integer ma_type [input] -// integer nelem [input] -// array(nelem) [input] -// -// logical function rtdb_get_info(handle, name, ma_type, nelem, date) -// integer handle [input] -// character *(*) name [input] -// integer ma_type [output] -// integer nelem [output] -// character*26 date [output] -// -// logical function rtdb_get(handle, name, ma_type, nelem, array) -// integer handle [input] -// character *(*) name [input] -// integer ma_type [input] -// integer nelem [input] -// array(nelem) [output] -// -// logical function rtdb_ma_get(handle, name, ma_type, nelem, ma_handle) -// integer handle [input] -// character *(*) name [input] -// integer ma_type [output] -// integer nelem [output] -// integer ma_handle [output] -// -// logical function rtdb_cput(handle, name, nelem, buf) -// integer handle [input] -// character *(*) name [input] -// character *(*) buf [input] -// -// logical function rtdb_cget(handle, name, nelem, buf) -// integer handle [input] -// character *(*) name [input] -// character *(*) buf [output] -// -// logical function rtdb_print(handle, print_values) -// integer handle [input] -// logical print_values [input] -// -// logical function rtdb_first(handle, name) -// integer handle [input] -// character *(*) name [output] -// -// logical function rtdb_next(handle, name) -// integer handle [input] -// character *(*) name [output] -// -// logical function rtdb_delete(handle, name) -// integer handle [input] -// character *(*) name [input] -// -bool rtdb_open, rtdb_close, rtdb_put, rtdb_get, rtdb_ma_get, - rtdb_cput, rtdb_cget, rtdb_print, rtdb_get_info, - rtdb_first, rtdb_next, rtdb_delete, rtdb_parallel, - rtdb_clone,rtdb_getfname,rtdb_cget_size; -//$Id$ -extern rtdb_open, rtdb_close, rtdb_put, rtdb_get, rtdb_ma_get, - rtdb_cput, rtdb_cget, rtdb_print, rtdb_get_info, - rtdb_first, rtdb_next, rtdb_delete, rtdb_parallel, - rtdb_clone,rtdb_getfname,rtdb_cget_size; -// -// Check these values against rtdb_f2c.c -// -const int rtdb_max_key=255; -const int rtdb_max_file=255; -// -const bool rtdb_seq_mode = false; -const bool rtdb_par_mode = true; +#ifndef _RTDB_H +#define _RTDB_H + +/* + All routines return TRUE (1) on success, FALSE (0) on failure. + + int rtdb_parallel(const int mode) + + Set the parallel access mode of all databases to mode and + return the previous setting + + + int rtdb_open(const char *filename, const char *mode, int *handle) + + Filename = path to file associated with the data base + mode = 'new' Open only if it does not exist already + 'old', Open only if it does exist already + 'unknown' Create new or open existing (preserving contents) + 'empty' Create new or open existing (deleting contents) + 'scratch' Create new or open existing (deleting contents) + and automatically delete upon closing. Also, items + cached in memory are not written to disk. + + handle = returns handle by which all future references to the + data base are made + + + + int rtdb_clone(const int handle, const char *suffix) + + Copy the data base file + + handle = handle to RTDB + suffix + + + int rtdb_close(const int handle, const char *mode) + + Close the data base + + handle = handle to RTDB + mode = 'keep' Preserve the data base file to enable restart + 'delete' Delete the data base file freeing all resources + + mode is overridden by opening the data base with + mode='scratch' in which instance it is always deleted + upon closing + + + int rtdb_get_info(const int handle, const char *name, int *ma_type, + int *nelem, char date[26]) + + Get info about an entry from the data base + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = returns MA type of the entry + nelem = returns no. of elements of the given type + date = returns date of insertion (null terminated character string) + + + int rtdb_put(const int handle, const char *name, const int ma_type, + const int nelem, const void *array) + + Insert an entry into the data base replacing previous entry + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = MA type of the entry + nelem = no. of elements of the given type + array = data to be inserted + + + int rtdb_get(const int handle, const char *name, const int ma_type, + const int nelem, void *array) + + Get an entry from the data base + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = MA type of the entry which must match entry type + nelem = size of array in units of ma_type + array = user provided buffer that returns data + + + int rtdb_ma_get(const int handle, const char *name, int *ma_type, + int *nelem, int *ma_handle) + + Get an entry from the data base returning an MA handle + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = returns MA type of the entry + nelem = returns no. of elements of type ma_type in data + ma_handle= returns MA handle to data + + + int rtdb_first(const int handle, const int namelen, char *name) + + Return the name of the first (user inserted) entry in the data base. + The order is effectively random. + + handle = handle to RTDB + namelen = size of user provided buffer name + name = name of entry is returned in this buffer + + + int rtdb_next(const int handle, const int namelen, char *name) + + Return the name of the next (user inserted) entry in the data base. + The order is effectively random. + + handle = handle to RTDB + namelen = size of user provided buffer name + name = name of entry is returned in this buffer + + + int rtdb_print(const int handle, const int print_values) + + Print the contents of the data base to stdout + + handle = handle to RTDB + print_values = boolean flag ... if true values as well as + keys are printed out. + + + int rtdb_delete(const int handle, const char *name) + + Delete the entry from the database. + Return + 1 if key was present and successfully deleted + + 0 if key was not present, or if an error occured + + handle = handle to RTDB + name = name of entry to delete + +*/ + +int rtdb_open(const char *, const char *, int *); +int rtdb_clone(const int, const char *); +int rtdb_getfname(const int, char [36]); +int rtdb_close(const int, const char *); +int rtdb_put(const int, const char *, const int, const int, + const void *); +int rtdb_get(const int, const char *, const int, const int, + bool); +int rtdb_get_info(const int, const char *, int *, int *, char [26]); +int rtdb_ma_get(const int, const char *, int *, int *, int *); +int rtdb_first(const int, const int, char *); +int rtdb_next(const int, const int, char *); +int rtdb_print(const int, const int); +int rtdb_delete(const int, const char *); +int rtdb_parallel(const int); + +/* + Following are 'sequential' versions of the above + for internal use only +*/ + +int rtdb_seq_open(const char *, const char *, int *); +int rtdb_seq_copy(const int, const char *); +int rtdb_seq_getfname(const int, char [36]); +int rtdb_seq_close(const int, const char *); +int rtdb_seq_put(const int, const char *, const int, const int, + const void *); +int rtdb_seq_get(const int, const char *, const int, const int, + void *); +int rtdb_seq_get_info(const int, const char *, int *, int *, char [26]); +int rtdb_seq_ma_get(const int, const char *, int *, int *, int *); +int rtdb_seq_first(const int, const int, char *); +int rtdb_seq_next(const int, const int, char *); +int rtdb_seq_print(const int, const int); +int rtdb_seq_delete(const int, const char *); + +#define RTDB_SEQ_MODE 0 //* Sequential mode +#define RTDB_PAR_MODE 1 //* Parallel mode + +#if (defined(CRAY) || defined(WIN32)) &&!defined(__crayx1) &&!defined(__MINGW32__) +#include "rtdb.cray.h" +#endif + +#endif diff --git a/src/tce/oce.py b/src/tce/oce.py index bba8979..31e1e14 100644 --- a/src/tce/oce.py +++ b/src/tce/oce.py @@ -27,9 +27,9 @@ def stringtooperatorsequence(expression): """Converts a string to an operatorsequence object""" # Syntax of the string is rather loosely defined as: # (1) Numerical factor (with no permutation allowed) (optional), summation (optional), amplitudes (optional), normal ordered sequence, - # (2) Numerical factor can be an arithmatic expression such as (1.0/4.0), + # (2) Numerical factor can be an arithmetic expression such as (1.0/4.0), # (3) Summation starts with either "SUM" or "sum" followed by a parenthesis of indexes, - # (4) Indexes can be either in one-letter notation (a-h, A-H for virtuals, i-o, I-O for occupieds, p-z, P-Z for either, case matters) + # (4) Indexes can be either in one-letter notation (a-h, A-H for virtuals, i-o, I-O for occupieds, p-z, P-Z for either, case matters) # or in OCE notation (p1,p2 for virtuals, h3,h4 for occupieds, g5,g6 for either, no overlap in numbering) # (5) Amplitudes start with "t" or any name followed by a dagger ("+") indicating complex conjugate (optional) and a parenthesis of indexes, # (6) Normal ordered operator sequence must exist even when it is empty "{}". @@ -71,8 +71,7 @@ def stringtooperatorsequence(expression): elif (index[0] == "g"): newsequence.append(Operator("general",dagger,int(index[1:]))) else: - print("Syntax error: an operator not recognized") - stop + raise SyntaxError(" an operator not recognized") operatorlist = operatorlist + newsequence newsequences.append(newsequence) @@ -156,8 +155,7 @@ def stringtooperatorsequence(expression): summation.indexes.append(indexinthelist) break else: - print("syntax error") - stop + raise SyntaxError(" ") # get amplitudes remainder = string.split(remainder,")") @@ -221,8 +219,7 @@ def stringtooperatorsequence(expression): newamplitude.indexes.append(indexinthelist) break else: - print("syntax error") - stop + raise SyntaxError(" ") amplitudes.append(newamplitude) newoperatorsequence = OperatorSequence(numericalfactor,summation,amplitudes,newsequences) @@ -231,8 +228,7 @@ def stringtooperatorsequence(expression): def combinepermutations(one,two): """Connects two permutations of indexes""" if (len(one) != len(two)): - print("Internal error") - stop + raise SyntaxError(" ") three = [] for n in range(len(one)/2): three.append(one[n]) @@ -749,7 +745,7 @@ class Factor: raise RuntimeError("unrealistic factor") fraction = abs(int(1.0/coefficient)) if (1.0/float(fraction) != abs(coefficient)): - print(" !!! WARNING !!! inaccurate arithmatic") + print(" !!! WARNING !!! inaccurate arithmetic") if (fraction == 1): frac = "" else: @@ -1732,7 +1728,7 @@ class ListOperatorSequences: print("") for line in self.show(): print(line) - return "" + return"" def show(self): """Returns a human-friendly string of the content""" @@ -1813,7 +1809,7 @@ class ListOperatorSequences: # pick up a pair of operator sequences for nsequencea in range(len(self.list)): # if (verbose): -# print('processing ',nsequencea,' / ',range(len(self.list))) +# print 'processing ',nsequencea,' / ',range(len(self.list)) sequencea = self.list[nsequencea] for nsequenceb in range(len(self.list)): sequenceb = self.list[nsequenceb] @@ -1907,7 +1903,7 @@ class ListOperatorSequences: print(" ! Warning! a cyclic contraction is found") # self.simplifythree(verbose) self.simplifytwo(verbose) - # the followings do not seem to affect the result, yet it costs enormous memory & time + # the following do not seem to affect the result, yet it costs enormous memory & time # self.simplifyfour(1) self = copy.deepcopy(self.deletezero()) return self diff --git a/src/tce/splitfiles.py b/src/tce/splitfiles.py index 75613a3..66ebdb8 100644 --- a/src/tce/splitfiles.py +++ b/src/tce/splitfiles.py @@ -1,32 +1,31 @@ -#!/usr/bin/env python3 # Usage: python splitfiles.py < inputfile.F # (c) All rights reserved by Battelle & Pacific Northwest Nat'l Lab (2002) # $Id$ -import string -import copy import sys source = sys.stdin.readlines() if (not source): - print("Usage: python splitfiles.py < inputfile.F") + print("Usage: python splitfiles.py < inputfile.F") nfiles = 0 +filename = " " +filecontent = " " for line in source: - if (string.find(line,"SUBROUTINE") != -1): + if (line.find("SUBROUTINE") != -1): if (nfiles): - file = open(filename+".F","w") + file = open(filename+".F", "w") for newline in filecontent: file.write(newline) - filename = string.split(line[string.find(line,"SUBROUTINE")+11:],"(")[0] + filename = line[line.find("SUBROUTINE")+11:].split("(", 99999)[0] print(filename+".o\\") nfiles = nfiles + 1 filecontent = [line] else: filecontent.append(line) # don't forget to dump the last subroutine -file = open(filename+".F","w") +file = open(filename+".F", "w") for newline in filecontent: file.write(newline) -print("Number of files generated:",nfiles) +print("Number of files generated:", nfiles) diff --git a/src/util/errquit.h b/src/util/errquit.h index 9c86292..53cc291 100644 --- a/src/util/errquit.h +++ b/src/util/errquit.h @@ -1,6 +1,8 @@ +#ifndef _ERRQUIT_H +#define _ERRQUIT_H // UERR - Not yet assigned to a category // UNKNOWN_ERR - Not yet assigned to a category -// MEM_ERROR - Generic Memory error +// MEM_ERR - Generic Memory error // RTDB_ERR - Error in the Runtime Database // INPUT_ERR - Error resulting from inproper user input // CAPMIS_ERR - Features that have not been implemented yet @@ -31,3 +33,5 @@ const int DISK_ERR = 100; const int CALC_ERR = 110; const int FMM_ERR = 120; // $Id$ + +#endif From efd354baf13fa639815627af9f065f144f10cfd1 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Wed, 6 Dec 2023 02:53:51 -0800 Subject: [PATCH 08/11] Began work on 'gradients' library --- Makefile | 40 ++++ src/Makefile | 16 ++ src/gradients/Makefile | 43 ++++ src/gradients/ga_reorder.c | 168 +++++++++++++++ src/gradients/grad1.c | 218 ++++++++++++++++++++ src/gradients/grad2.c | 0 src/gradients/grad_dens.c | 0 src/gradients/grad_force.c | 0 src/gradients/grad_getdens.c | 0 src/gradients/grad_inp.c | 0 src/gradients/grad_store.c | 0 src/gradients/gradients.c | 128 ++++++++++++ src/gradients/scf_gradient.c | 35 ++++ src/nwchem.c | 385 ++++++++++++++++++++++++----------- src/rtdb/Makefile | 39 ++++ src/rtdb/context.c | 210 +++++++++++++++++++ src/rtdb/context.h | 14 ++ src/rtdb/davetest.c | 15 ++ src/rtdb/rtdb.cray.h | 26 +++ src/rtdb/testgr.c | 32 +++ src/util/global.h | 11 + src/util/printlevels.h | 12 ++ src/util/stdio.h | 56 +++++ src/util/util.h | 11 + 24 files changed, 1340 insertions(+), 119 deletions(-) create mode 100644 Makefile create mode 100644 src/Makefile create mode 100644 src/gradients/Makefile create mode 100644 src/gradients/ga_reorder.c create mode 100644 src/gradients/grad1.c create mode 100644 src/gradients/grad2.c create mode 100644 src/gradients/grad_dens.c create mode 100644 src/gradients/grad_force.c create mode 100644 src/gradients/grad_getdens.c create mode 100644 src/gradients/grad_inp.c create mode 100644 src/gradients/grad_store.c create mode 100644 src/gradients/gradients.c create mode 100644 src/gradients/scf_gradient.c create mode 100644 src/rtdb/Makefile create mode 100644 src/rtdb/context.c create mode 100644 src/rtdb/context.h create mode 100644 src/rtdb/davetest.c create mode 100644 src/rtdb/rtdb.cray.h create mode 100644 src/rtdb/testgr.c create mode 100644 src/util/global.h create mode 100644 src/util/printlevels.h create mode 100644 src/util/stdio.h create mode 100644 src/util/util.h diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..b65cd60 --- /dev/null +++ b/Makefile @@ -0,0 +1,40 @@ +CC = gcc +CXX = g++ + +MPICC = mpicc +MPICXX = mpicxx + +NWCHEM_TOP = $(shell pwd) + +SRC = $(NWCHEM_TOP)/src +BIN = $(NWCHEM_TOP)/bin +BUILD = $(NWCHEM_TOP)/build + +LIB_DEFINES = -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" \ + -DCOMPILATION_DIR="'$(TOPDIR)'" \ + -DNWCHEM_BRANCH="'$(CODE_BRANCH)'" + +CFLAGS=-c -Wall +LDFLAGS= + +export + +TARGETS=nwchem + +#TARGETS := $(addprefix $(BIN)/, $(TARGETS)) + +.PHONY: all clean + +all: $(TARGETS) + +nwchem: + $(MAKE) -C $(SRC) + +clean: + rm $(BIN)/$(TARGETS) + rm $(BUILD)/*.o + +dist-clean: clean + rmdir $(BIN) + rmdir $(BUILD) + diff --git a/src/Makefile b/src/Makefile new file mode 100644 index 0000000..7628ae5 --- /dev/null +++ b/src/Makefile @@ -0,0 +1,16 @@ + +SOURCES= +LIBRARIES= + +libs: $(LIBRARY_PATH) + @mkdir -p $(LIB) + +$(BIN)/nwchem: $(BUILD)/nwchem.o libs + @mkdir -p $(@D) + $(MPICC) $(LDFLAGS) $^ -o $@ + +$(BUILD)/%.o: $(SRC)/%.c + @mkdir -p $(@D) + $(MPICC) $(CFLAGS) -I$(SRC) -c $< -o $@ + + diff --git a/src/gradients/Makefile b/src/gradients/Makefile new file mode 100644 index 0000000..2fe9d8e --- /dev/null +++ b/src/gradients/Makefile @@ -0,0 +1,43 @@ + +# OBJ = gradients.o grad_force.o grad1.o scf_gradient.o \ + grad_dens.o grad_inp.o ga_reorder.o +# OBJ_OPTIMIZE = grad2.o grad_getdens.o + +# USES_BLAS = grad2.F ga_reorder.F grad_dens.F + +# LIBRARY = libgradients.a + +#include ../config/makefile.h +#include ../config/makelib.h + + + +CC=gcc + +BUILD = /people/parl703/nwchem/build + +SRC = $(shell pwd) + +LIB = /people/parl703/nwchem/lib + + + + +SOURCES := $(wildcard *.c) +# OBJECTS := $(patsubst %.c, ../../build/%.o, $(SOURCES)) +# OBJ_BUILD = $(addprefix $(BUILD)/, $(OBJ) $(OBJ_OPTIMIZE)) + +OBJ := $(addprefix $(BUILD)/, $(OBJ)) +OBJ_OPTIMIZE := $(addprefix $(BUILD)/, $(OBJ_OPTIMIZE)) + +all: libgradients + +libgradients: object object_opt + ar -cvrsu $(LIB)/libgradients.a $(OBJ) $(OBJ_OPTIMIZE) + +object: $(OBJ) + +object_opt: $(OBJ_OPTIMIZE) + +$(BUILD)/%.o: %.c + $(CC) -I$(SRC) -c $< -o $@ \ No newline at end of file diff --git a/src/gradients/ga_reorder.c b/src/gradients/ga_reorder.c new file mode 100644 index 0000000..10cde0f --- /dev/null +++ b/src/gradients/ga_reorder.c @@ -0,0 +1,168 @@ +#include + +#include "../util/errquit.h" +//#include "global.h" +#include "../util/global.h" + +void ga_reorder(int g_a, bool orow, int *rmap, bool ocol, int *cmap) { + + int g_d, i, j, l_v, k_v, l_vv, k_vv, ma_type, dim1, dim2, jj; + + ga_inquire(g_a, ma_type, dim1, dim2); + + if (!ma_alloc_get(MT_DBL, dim1, "gareo", l_v, k_v)) { + errquit("ga_reorder: could not allocate column", dim1, MA_ERR); + } + + if (!ma_alloc_get(MT_DBL, dim1, "gareo", l_vv, k_vv)) { + errquit("ga_reorder: could not allocate column2", dim1, MA_ERR); + } + + ga_sync(); + if (!ga_duplicate(g_a, g_d, "ga_reorder")) { + errquit("ga_reorder: duplicate failed", 0, GA_ERR); + } + ga_copy(g_a, g_d); + + for (j = ga_nodeid(); j < dim2; j += ga_nnodes()) { + if (orow) { + ga_get(g_d, 1, dim1, j, j, dbl_mb[k_v], dim1); + for (i = 0; i < dim1; i++) { + dbl_mb[k_vv+rmap[i]-1] = dbl_mb[k_v+i-1]; + } + } else { + ga_get(g_d, 1, dim1, j, j, dbl_mb[k_vv], dim1); + } + jj = j; + if (ocol) {jj = cmap[j];} + ga_put(g_a, 1, dim1, jj, jj, dbl_mb[k_vv], dim1); + } + + if (!ma_free_heap(l_vv)) { + errquit("ga_reo: ma?", 0, MA_ERR); + } + + if (!ma_free_heap(l_v)) { + errquit("ga_reo: ma2?", 0, MA_ERR); + } + + if (!ga_destroy(g_d)) { + errquit("ga_reo: ga_destroy?", 0, GA_ERR); + } + +} + +void nga_reorder(int g_a, bool orow, int *rmap, bool ocol, int *cmap) { + /* + This is basically just an extension of ga_reorder and is not very + generic at this point. As a matter of fact, it assumes (and tests) + that the dimension is 3 and that you only want to reorder the last + two indices. This can be made more general after I test this version. + Also, I am wasting a lot of memory by duplicating the whole ga. This + will need to be optimized in the future. + */ + + int g_d, i, j, l_v, k_v, l_vv, k_vv, ma_type; + int dim0, dim1, dim2, jj; + int ndim, dims[3], lo[3], hi[3], ld[2]; + + ndim = ga_ndim(g_a); + if (ndim != 3) { + errquit("nga_reorder: must have 3 dimensions", ndim, GA_ERR); + } + nga_inquire(g_a, ndim, dims); + dim1 = dims[1]; + dim2 = dims[2]; + + if (!ma_alloc_get(MT_DBL, dim1, "gareo", l_v, k_v)) { + errquit("ga_reorder: could not allocate column", dim1, GA_ERR); + } + if (!ma_alloc_get(MT_DBL, dim1, "gareo", l_vv, k_vv)) { + errquit("ga_reorder: could not allocate column2", dim1, GA_ERR); + } + + ga_sync(); + if (!ga_duplicate(g_a, g_d, "ga_reorder")) { + errquit("ga_reorder: duplicate failed", 0, GA_ERR); + } + ga_copy(g_a, g_d); + + ld[0] = 1; + lo[1] = 1; + hi[1] = dim1; + ld[1] = dim1; + for (dim0 = 0; dim0 < dims[0]; i++) { + lo[0] = dim0; + hi[0] = dim0; + for (j = ga_nodeid(); j < dim2; j += ga_nnodes()) { + lo[2] = j; + hi[2] = j; + if (orow) { + nga_get(g_d, lo, hi, dbl_mb[k_v], ld); + for (i = 0; i < dim1; i++) { + dbl_mb[k_vv+rmap[i]-1] = dbl_mb[k_v+i-1]; + } + } else { + nga_get(g_d, lo, hi, dbl_mb[k_vv], ld); + } + + jj = j; + if (ocol) {jj = cmap[j];} + lo[2] = jj; + hi[2] = jj; + nga_put(g_a, lo, hi, dbl_mb[k_vv], ld); + } + } + + if (!ma_free_heap(l_vv)) errquit("ga_reo: ma?", 0, MA_ERR); + if (!ma_free_heap(l_v)) errquit("ga_reo: ma2?", 0,MA_ERR); + ga_sync(); + if (!ma_free_heap(g_d)) errquit("ga_reo: ga_destroy", 0, GA_ERR); + +} + +void matrix_reorder(int dim1, int dim2, double *a, bool orow, int *rmap, bool ocol, int *cmap) { + + int i, j, l_v, k_v, l_vv, k_vv, jj; + int l_d, k_d; + + if (!ma_alloc_get(MT_DBL, dim1*dim2, "mareo", l_d, k_d)) { + errquit("ga_reorder: could not allocate dup", dim1*dim2, MA_ERR); + } + + if (!ma_alloc_get(MT_DBL, dim1, "mareo", l_v, k_v)) { + errquit("ga_reorder: could not allocate column", dim1, MA_ERR); + } + + if (!ma_alloc_get(MT_DBL, dim1, "mareo", l_vv, k_vv)) { + errquit("ga_reorder: could not allocate column2", dim1, MA_ERR); + } + + dcopy(dim1*dim2, a, 1, dbl_mb[k_d], 1); + + for (j = 0; j < dim2; j++) { + if (orow) { + dcopy(dim1, dbl_mb[k_d+j*dim1], 1, dbl_mb[k_v], 1); + for (i = 0; i < dim1; i++) { + dbl_mb[k_vv+rmap[i]-1] = dbl_mb[k_v+i-1]; + } + } else { + dcopy(dim1, dbl_mb[k_d+j*dim1], 1, dbl_mb[k_vv], 1); + } + jj = j; + if (ocol) jj = cmap[j]; + dcopy(dim1, dbl_mb[k_vv], 1, a[jj], 1); + } + + if (!ma_free_heap(l_vv)) { + errquit("ma_reo: ma?", 0, MA_ERR); + } + + if (!ma_free_heap(l_v)) { + errquit("ma_reo: ma2?", 0, MA_ERR); + } + + if (!ma_free_heap(l_d)) { + errquit("ma_reo: ma?", 0, MA_ERR); + } +} \ No newline at end of file diff --git a/src/gradients/grad1.c b/src/gradients/grad1.c new file mode 100644 index 0000000..7ca8436 --- /dev/null +++ b/src/gradients/grad1.c @@ -0,0 +1,218 @@ +#include + +#include "../util/global.h" +//#include "geom.h" +//#include "bas.f" +//#include "rtdb.h" +//#include "sym.h" +//#include "bq_params.h" + +#define NO_BQGEM 1 + +void grad1(double *H, int lbuf, double *scr, int lscr, double *dens, + double *wdens, double *frc_nuc, double *frc_kin, double *frc_wgh, + int g_force, int *g_dens, int g_wdens, int basis, int geom, int nproc, + int nat, int max_at_bf, int rtdb, bool oskel, int ndens ) { + + int ijatom, next, iat1, iat2, iat3, ish1, ish2, + iab1f, iab1l, iab2f, iab2l, iac1f, iac1l, iac2f, iac2l, + if1, il1, if2, il2, icart, ic, nint, ip1, ip2; + + double crd1[3], crd2[3]; // atomic coordinates; + + int idatom[2]; + + double dE, dx, dy, dz, qfac, fact, q1, q2; + + bool status, pointforce, dobq; + + char name[16]; + + int bq_ncent; + int i_qbq,i_cbq; + double r12; + + int task_size; + +// AJL/Begin/SPIN ECPs + int ecp_channels; + int iecp; + double H_beta[lbuf]; + double dens_beta[max_at_bf][max_at_bf]; +#ifdef NO_BQGEM +//#include "inp.h" + char bqchar[2]; +#endif + +// Read this value from rtdb vvvv + if (!rtdb_get(rtdb, "dft:spin_polarised_ecps'", MT_INT, 1, ecp_channels)) { + ecp_channels = 1; + } + +/* AJL: With spin-polarised ECPs Hcore will be spin dependent + See Szabo and Ostlund pg. 215 + So we need to separate out the densities + + if (ecp_channels.gt.1) then + + Restore alpha and beta densities to calculate spin-polarised + derivatives + + call ga_print(g_dens(1)) + call ga_print(g_dens(2)) + call ga_dadd(1d0, g_dens(1), -1d0, g_dens(2), g_dens(1)) + call ga_print(g_dens(1)) + call ga_print(g_dens(2)) + end if + AJL/End */ + + task_size = 1; + status = rtdb_parallel(true); // Broadcast reads to all processes + + pointforce = geom_include_bqbq(geom); + dobq = geom_extbq_on(); + hf_print_set(1); + + ijatom = -1; + next = nxtask(nproc,task_size); + for (iat1 = 0; iat1 < nat; iat1++) { + for (iat2 = 0; iat2 < iat1; iat2++) { + ijatom++; + if (ijatom == next) { + status = bas_ce2bfr(basis,iat1,iab1f,iab1l); + status = bas_ce2bfr(basis,iat2,iab2f,iab2l); + + if (iab1f <= 0 || iab2f <= 0) { + // At least one center has no functions on it ... next atom + goto g1010; + } + + if (oskel) { + if (!sym_atom_pair(geom, iat1, iat2, qfac)) goto g1010; + } else { + qfac = 1.0; + } + + status = bas_ce2cnr(basis,iat1,iac1f,iac1l); + status = bas_ce2cnr(basis,iat2,iac2f,iac2l); + + // AJL/Begin/SPIN ECPs + // call ga_get(g_dens,iab1f,iab1l,iab2f,iab2l,dens,max_at_bf) + for (iecp = 0; iecp < ecp_channels; iecp++) { + if (iecp == 1) { + ga_get(g_dens[iecp],iab1f,iab1l, iab2f,iab2l,dens,max_at_bf); + } else { + ga_get(g_dens[iecp],iab1f,iab1l, iab2f,iab2l,dens_beta,max_at_bf); + } + } + // Recombine g_dens, as it is not used again + // if (ecp_channels.gt.1) then + // call ga_dadd(1d0, g_dens(1), 1d0, g_dens(2), g_dens(1)) + // end if + // g_wdens is not dependent on spin, so can leave this + ga_get(g_wdens,iab1f,iab1l,iab2f,iab2l,wdens,max_at_bf); + // AJL/End + + for (ish1 = iac1f; ish1 < iac1l; ish1++) { + if ( iat1 == iat2 ) iac2l = ish1; + for (ish2 = iac2f; ish2 < iac2l; ish2++) { + // shell block in atomic (D/Dw)-matrix block + status = bas_cn2bfr(basis,ish1,if1,il1); + if1 = if1 - iab1f + 1; + il1 = il1 - iab1f + 1; + status = bas_cn2bfr(basis,ish2,if2,il2); + if2 = if2 - iab2f + 1; + il2 = il2 - iab2f + 1; + + nint = ( il1 - if1 + 1 ) * ( il2 - if2 + 1 ); + + // overlap derivatives + intd_1eov(basis,ish1,basis,ish2,lscr,scr, lbuf,H,idatom); + + // Dw x S + if ( idatom[0] >= 1 ) { + // idatom(1).ge.0 <=> idatom(2).ge.0 (no check necessary) + ic = 0; + for (icart = 0; icart < 3; icart++) { + dE = 0.0; + for (ip1 = if1; ip1 < il1; ip1++) { + for (ip2 = if2; ip2 < il2; ip2++) { + dE += wdens[ip1*il1+ip2] * H[ic]; + } + } + dE = dE * qfac; + frc_wgh[3*icart+idatom[0]] = frc_wgh[3*icart+idatom[0]] - dE - dE; + frc_wgh[3*icart+idatom[1]] = frc_wgh[3*icart+idatom[1]] + dE + dE; + } + } + // 1el. derivatives + if (!dobq) { + intd_1eh1(basis,ish1,basis,ish2,lscr,scr,lbuf,H); + } else { + intd_1epot(basis,ish1,basis,ish2,lscr,scr,lbuf,H); + } + + // AJL/Begin/SPIN ECPs + // With spin-polarised ECPs Hcore will be spin dependent + // See Szabo and Ostlund pg. 215 + if (ecp_channels > 1) { + // 1el. derivatives + if (!dobq) { + // For now this will do, but this could be more efficiently done + intd_1eh1_beta(basis,ish1,basis,ish2,lscr,scr,lbuf,H_beta); + } else { + intd_1epot_beta(basis,ish1,basis,ish2,lscr,scr,lbuf,H_beta); + } + } + // AJL/End + + // D x H + ic = 0; + for (iat3 = 0; iat3 < nat; iat3++) { + for (icart = 0; icart < 3; icart++) { + dE = 0.0; + + } + } + } + } + } + + g1010: continue; + } + } + + + +} + +/* +C> \brief calculate the gradient terms due to the interaction with the +C> COSMO charges +C> +C> Evaluate the gradient contributions from the COSMO embedding. The +C> original part is from Klamt and Schüürmann [1] +C> (see Eqs.(13-16)). The derivatives of matrix \f$A\f$ have been +C> modified by York and Karplus [2] (see Eqs.(73-76)) to obtain smooth +C> potential energy surfaces. York and Karplus also modified matrix +C> \f$B\f$ which is easy to do in their classical force field code. +C> In an ab-initio code this not so easy to do and as it is not +C> required to eliminate singularities the original expression from [1] +C> for \f$B\f$ is used here. +C> +C> ### References ### +C> +C> [1] A. Klamt, G. Schüürmann, +C> "COSMO: a new approach to dielectric screening in solvents with +C> explicit expressions for the screening energy and its gradient", +C> J. Chem. Soc., Perkin Trans. 2, 1993, pp 799-805, DOI: +C> +C> 10.1039/P29930000799. +C> +C> [2] D.M. York, M. Karplus, +C> "A smooth solvation potential based on the conductor-like +C> screening model", J. Phys. Chem. A (1999) 103, +C> pp 11060-11079, DOI: +C> +C> 10.1021/jp992097l. +*/ \ No newline at end of file diff --git a/src/gradients/grad2.c b/src/gradients/grad2.c new file mode 100644 index 0000000..e69de29 diff --git a/src/gradients/grad_dens.c b/src/gradients/grad_dens.c new file mode 100644 index 0000000..e69de29 diff --git a/src/gradients/grad_force.c b/src/gradients/grad_force.c new file mode 100644 index 0000000..e69de29 diff --git a/src/gradients/grad_getdens.c b/src/gradients/grad_getdens.c new file mode 100644 index 0000000..e69de29 diff --git a/src/gradients/grad_inp.c b/src/gradients/grad_inp.c new file mode 100644 index 0000000..e69de29 diff --git a/src/gradients/grad_store.c b/src/gradients/grad_store.c new file mode 100644 index 0000000..e69de29 diff --git a/src/gradients/gradients.c b/src/gradients/gradients.c new file mode 100644 index 0000000..bbee526 --- /dev/null +++ b/src/gradients/gradients.c @@ -0,0 +1,128 @@ +#include +#include +#include + + + +#include "../util/errquit.h" +//#include "bas.h" +//#include "geom.h" +#include "../util/global.h" +#include "../rtdb/rtdb.h" +//#include "schwarz.h" +#include "../util/util.h" +#include "../util/stdio.h" + +bool gradients(int rtdb) { + + int mt_log; + + // gradients module. + + /* + Assumes SCF has been completed, MO vectors stored + and all information is still in the RTDB + */ + + int geom, basis; // handles + bool status; + char title[255]; + + bool odbug; + bool ocosmo; + bool osome; + + status = rtdb_parallel(true); // Broadcast reads to all processes + ecce_print_module_entry("gradients"); + + // Extract high level info from the data-base setting defaults + + if (!rtdb_cget(rtdb, "title", 1, title)) strncpy(title, " ", 4); + if (!geom_create(geom, "geometry")) errquit("gradients: geom_create?", 0, GEOM_ERR); + if (!geom_rtdb_load(rtdb, geom, "geometry")) errquit("gradients: no geometry ", 0, GEOM_ERR); + if (!bas_create(basis, "ao basis")) errquit("gradients: bas_create?", 0, BASIS_ERR); + if (!bas_rtdb_load(rtdb, geom, basis, "ao basis")) errquit("gradients: no ao basis", 0, BASIS_ERR); + if (!int_normalize(rtdb,basis)) errquit("gradients: normalization failed", 911, INT_ERR); + + /* + Figure out the numer of electrons from the required total + charge and the sum of nuclear charges + + if (.not. rtdb_get(rtdb, 'charge', MT_DBL, 1, charge)) + $ charge = 0.0d0 + */ + + if (nodeid == 0) { + if (util_print("information", print_low)) { + util_print_centered(LuOut, "NWChem Gradients Module", 40, true); + fprintf(stdout, "%s", LuOut); + util_flush(); + } + if (util_print("information", print_medium)) { + fprintf(stdout, "%s", LuOut); + if (title != " ") { + util_print_centered(LuOut, title, 40, false); + fprintf(stdout, "%s", LuOut); + } + util_flush(LuOut); + } + if (util_print("geometry", print_high)) { + if (!geom_print(geom)) { + errquit("gradients: geom_print ?", 0, GEOM_ERR); + } + util_flush(LuOut); + } + if (uitl_print("basis", print_high)) { + if (!bas_print(basis)) { + errquit("gradients: bas_print ?", 0, BASIS_ERR); + } + util_flush(LuOut); + } + } + + odbug = false; + odbug = odbug && ga_nodeid() == 0; + if (rtdb_get(rtdb,"slv:cosmo", mt_log, 1, ocosmo)) { + if (odbug) { + fprintf(stdout, "-cosmo- ... found in -gradients-%s %d", + ocosmo ? "true" : "false", ga_nodeid()); + } + if (ocosmo) { + if (odbug) { + osome = true; + } else { + osome = false; + } + osome = osome && ga_nodeid() == 0; + if (odbug) { + fprintf(stdout, "-cosmo- ... found and .true. %s %d", + ocosmo ? "true" : "false", ga_nodeid()); + } + } else { + if (odbug) { + fprintf(stdout, "-cosmo- ... found but .false. %s %d", + ocosmo ? "true" : "false", ga_nodeid()); + } + } + } else { + if (odbug) { + fprintf(stdout, "-cosmo- not found in -gradients-"); + } + } + ga_sync(); + + // go for it ... finally ... + + grad_force(rtdb, basis, geom); + + // gradients is done destroy basis and geometry handles + // (e.g., preserve the memory available to other modules!!) + + if ( !(bas_destroy(basis) && geom_destroy(geom)) ) { + errquit("gradients:error destroying geom and basis handles",911, GEOM_ERR); + } + + ecce_print_module_exit("gradients","ok"); + + return true; +} \ No newline at end of file diff --git a/src/gradients/scf_gradient.c b/src/gradients/scf_gradient.c new file mode 100644 index 0000000..620f492 --- /dev/null +++ b/src/gradients/scf_gradient.c @@ -0,0 +1,35 @@ +#include + + +#include "../rtdb/rtdb.h" +#include "../util/errquit.h" + +bool mcscf_gradient(int rtdb) { + if (!mcscf(rtdb)) { + errquit("mcscf_gradient: mcscf energy failed", 0, CALC_ERR); + } + + util_print_push(); + util_print_rtdb_load(rtdb,"mcscf"); + if(!gradients(rtdb)) { + errquit("mcscf_gradient: gradients failed", 0, CALC_ERR); + } + util_print_pop(); + + return true; +} + +bool scf_gradient(int rtdb) { + + if (!scf(rtdb)) { + errquit("scf_gradient: scf energy failed", 0, CALC_ERR); + } + util_print_push(); + util_print_rtdb_load(rtdb, "scf"); + if (!gradients(rtdb)) { + errquit("scf_gradient: gradients failed", 0, CALC_ERR); + } + util_print_pop(); + + return true; +} \ No newline at end of file diff --git a/src/nwchem.c b/src/nwchem.c index e98437a..26409c1 100644 --- a/src/nwchem.c +++ b/src/nwchem.c @@ -28,50 +28,51 @@ int32_t IO_CODE; #endif -// $Id$ +/* + $Id$ -// ====================================================================================================== -//> \mainpage Northwest Computational Chemistry Package (NWChem) 7.0.2 -//> -//> NWChem is an open-source computational chemistry package distributed under the terms of -//> the Educational Community License (ECL) 2.0 -//> -//> This software and its documentation were developed at the EMSL at Pacific Northwest National Laboratory, -//> a multiprogram national laboratory, operated for the U.S. Department of Energy by Battelle under -//> Contract Number DE-AC05-76RL01830. Support for this work was provided by the Department of Energy -//> Office of Biological and Environmental Research, Office of Basic Energy Science, and the Office of -//> Advanced Scientific Computing. -//> -//> Licensed under the Educational Community License, Version 2.0 (the "License"); you may -//> not use this file except in compliance with the License. You may obtain a copy of the -//> License at https://opensource.org/licenses/ECL-2.0. -//> -//> Unless required by applicable law or agreed to in writing, software distributed under the -//> License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, -//> either express or implied. See the License for the specific language governing -//> permissions and limitations under the License. -//> -//> Further information, including user documentation and forums, may be found at -//> http://www.nwchem-sw.org/. Alternatively, -//> the paper -//> -//> * M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. Van Dam, -//> D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong (2010)
-//> "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations"
-//> Computer Physics Communications, 181, 1477–1489, DOI: 10.1016/j.cpc.2010.04.018 -//> -//> provides details on the codes capabilities. -//> -//> Copyright (c) 1994-2020 Pacific Northwest National Laboratory, Battelle Memorial Institute -//> -//> Environmental Molecular Sciences Laboratory (EMSL)
-//> Pacific Northwest National Laboratory
-//> Richland, WA 99352 + ===================================================================================================== + \mainpage Northwest Computational Chemistry Package (NWChem) 7.0.2 -// ====================================================================================================== + NWChem is an open-source computational chemistry package distributed under the terms of + the Educational Community License (ECL) 2.0 + This software and its documentation were developed at the EMSL at Pacific Northwest National Laboratory, + a multiprogram national laboratory, operated for the U.S. Department of Energy by Battelle under + Contract Number DE-AC05-76RL01830. Support for this work was provided by the Department of Energy + Office of Biological and Environmental Research, Office of Basic Energy Science, and the Office of + Advanced Scientific Computing. -int main(){ + Licensed under the Educational Community License, Version 2.0 (the "License"); you may + not use this file except in compliance with the License. You may obtain a copy of the + License at https://opensource.org/licenses/ECL-2.0. + + Unless required by applicable law or agreed to in writing, software distributed under the + License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, + either express or implied. See the License for the specific language governing + permissions and limitations under the License. + + Further information, including user documentation and forums, may be found at + http://www.nwchem-sw.org/. Alternatively, + the paper + + * M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. Van Dam, + D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong (2010)
+ "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations"
+ Computer Physics Communications, 181, 1477–1489, DOI: 10.1016/j.cpc.2010.04.018 + + provides details on the codes capabilities. + + Copyright (c) 1994-2020 Pacific Northwest National Laboratory, Battelle Memorial Institute + + Environmental Molecular Sciences Laboratory (EMSL)
+ Pacific Northwest National Laboratory
+ Richland, WA 99352 + + ===================================================================================================== +*/ + +int main(int argc, char *argv[]) { char input_filename[nw_max_path_len], rtdb_name[nw_max_path_len]; double total_wall, total_cpu; #ifdef USE_OFFLOAD @@ -90,26 +91,26 @@ int main(){ extern omp_get_max_threads; #endif -// Create parallel processes and initialize IPC layer + // Create parallel processes and initialize IPC layer pbeginf(); -// MXINIT is needed by PeIGS and PFFT to initialize -// the communication fabric they use. + // MXINIT is needed by PeIGS and PFFT to initialize + // the communication fabric they use. mxinit(); -// Initialize timers so they are relative to job start + // Initialize timers so they are relative to job start total_wall = -util_wallsec(); total_cpu = -util_cpusec(); -// Only process 0 opens the input file -// (note that ga_nodeid() does not work yet!) + // Only process 0 opens the input file + // (note that ga_nodeid() does not work yet!) if (nodeid() == 0){ -// Get the name of the input file from the command line + // Get the name of the input file from the command line get_input_filename(input_filename); @@ -126,17 +127,17 @@ int main(){ #endif } -// Look for memory directive in the input ... must eventually -// open the rtdb first so that can get memory directive out of that -// if it is not in the input + // Look for memory directive in the input ... must eventually + // open the rtdb first so that can get memory directive out of that + // if it is not in the input -// The user input model has well-defined categories of memory, -// each of which has a specific size. How we use these limits -// depends on the platform we are running on. + // The user input model has well-defined categories of memory, + // each of which has a specific size. How we use these limits + // depends on the platform we are running on. input_mem_size(stack, heap, global, overify, ohardfail); -// Initialize local memory allocator & global array tools + // Initialize local memory allocator & global array tools ga_initialize_ltd(ma_sizeof(mt_dbl,global,mt_byte)); // this must happen after GA and before MA @@ -150,20 +151,21 @@ int main(){ errquit('nwchem.F: ma_init failed (ga_uses_ma=F)',911, MA_ERR); } } + /* + Touch OpenMP here so that any runtime initialization happens up-front. + This ensures that any printout that the OpenMP runtime generates, + such as affinity information, appears at the top of the output file. + Otherwise, it might not appear until e.g. the CCSD module, at which + point it will pollute the output file in an undesirable way. -// Touch OpenMP here so that any runtime initialization happens up-front. -// This ensures that any printout that the OpenMP runtime generates, -// such as affinity information, appears at the top of the output file. -// Otherwise, it might not appear until e.g. the CCSD module, at which -// point it will pollute the output file in an undesirable way. + Do not move this in front of GA/MPI/TCGMSG initialization, since the + OpenMP runtime may inherit affinity information from MPI that is only + determined during MPI initialization. -// Do not move this in front of GA/MPI/TCGMSG initialization, since the -// OpenMP runtime may inherit affinity information from MPI that is only -// determined during MPI initialization. - -// Format definition is outside of preprocessor protection to ensure the -// label is not accidentally reused, since that will not be caught by -// testing that does not enable OpenMP. + Format definition is outside of preprocessor protection to ensure the + label is not accidentally reused, since that will not be caught by + testing that does not enable OpenMP. + */ g99 format(2x, 'NWChem w/ OpenMP: Maximum threads = ',i4); #if defined(USE_OPENMP){ @@ -176,71 +178,71 @@ int main(){ } } #endif -// set no. threads for threaded BLAS to 1 + // set no. threads for threaded BLAS to 1 util_blas_set_num_threads(1); rtdb_init() -// More for amusement then efficiency force all MA allocated entities -// to be aligned at the beginning of a 128 byte cache line + // More for amusement then efficiency force all MA allocated entities + // to be aligned at the beginning of a 128 byte cache line -// if (!ma_set_numalign(7)){ -// errquit('nwchem.cpp: ma_set_numalign failed',911, MA_ERR); -// } -// aligned to 64byte record + // if (!ma_set_numalign(7)){ + // errquit('nwchem.cpp: ma_set_numalign failed',911, MA_ERR); + // } + // aligned to 64byte record if (!ma_set_numalign(6)){ errquit('nwchem.cpp: ma_set_numalign failed', 911, MA_ERR); } + /* + old:------------------------------------------------------- START --------- + old:C GA allocations come out of MA space, so lump them together + old:C and let MA impose the limits on GA sizes instead of actually + old:C using the global limit. + old:C + old: if ( ga_uses_ma() ) then + old: if (.not. ma_init(mt_dbl, stack, heap+global)) + old: $ call errquit('nwchem: ma_init failed', -1) + old: call ga_initialize + old:C + old:C GA allocations are separate from MA, so the separate limit + old:C must be enforced. Note GA only understands bytes. + old:C + old: else + old: if (.not. ma_init(mt_dbl, stack, heap)) + old: $ call errquit('nwchem: ma_init failed', -1) + old: call ga_initialize_ltd(ma_sizeof(mt_dbl, global, mt_byte) ) + old: endif + old:------------------------------------------------------- END ----------- + */ + //*** call nxtval_ga_initialize() -//old:------------------------------------------------------- START --------- -//old:C GA allocations come out of MA space, so lump them together -//old:C and let MA impose the limits on GA sizes instead of actually -//old:C using the global limit. -//old:C -//old: if ( ga_uses_ma() ) then -//old: if (.not. ma_init(mt_dbl, stack, heap+global)) -//old: $ call errquit('nwchem: ma_init failed', -1) -//old: call ga_initialize -//old:C -//old:C GA allocations are separate from MA, so the separate limit -//old:C must be enforced. Note GA only understands bytes. -//old:C -//old: else -//old: if (.not. ma_init(mt_dbl, stack, heap)) -//old: $ call errquit('nwchem: ma_init failed', -1) -//old: call ga_initialize_ltd(ma_sizeof(mt_dbl, global, mt_byte) ) -//old: endif -//old:------------------------------------------------------- END ----------- + // Trap SIGFPE after GA to override handler -//*** call nxtval_ga_initialize() - -// Trap SIGFPE after GA to override handler - -//*** call ieeetrap() + //*** call ieeetrap() #if defined(LINUXALPHA) dec_fpe(); // To avoid underflow problems on Alpha in Texas #endif #ifdef CRAY_T3D - // This as a temporary fix for SIGFPE in Texas that does not seem - // to affect the final results + // This as a temporary fix for SIGFPE in Texas that does not seem + // to affect the final results oldact = fsigctl('IGNORE','SIGFPE',0); #endif #ifdef LINUX -// uncommenting this line turns on sigfpe trapping under linux -// linux_trapfpe(); + // uncommenting this line turns on sigfpe trapping under linux + // linux_trapfpe(); #endif #ifdef MACX -// uncommenting this line turns on sigfpe trapping under Mac OSX -// macx_trapfpe(); + // uncommenting this line turns on sigfpe trapping under Mac OSX + // macx_trapfpe(); #endif -// Hard fail is good for development but means that we cannot -// respond to allocation problems. Disable by default. + // Hard fail is good for development but means that we cannot + // respond to allocation problems. Disable by default. status = ma_set_auto_verify(overify); status = ma_set_hard_fail(ohardfail); status = ma_set_error_print(ohardfail); -// Initialize pstat + // Initialize pstat if (!pstat_init(20,1,' ')){ errquit('nwchem: pstat_init failed', 0, UNKNOWN_ERR); @@ -248,13 +250,13 @@ int main(){ input_file_info(input_filename, rtdb_name, ostartup, ocontinue); -// Now are ready to summarize the environment + // Now are ready to summarize the environment nwchem_banner(input_filename, rtdb_name, ostartup, ocontinue); -// Actually open the database and store the file prefix + // Actually open the database and store the file prefix -// Note that only process 0 has the database name ... that is OK. + // Note that only process 0 has the database name ... that is OK. if (ostartup){ if (!rtdb_open(rtdb_name, 'empty', rtdb)){ @@ -267,12 +269,12 @@ int main(){ } -// initialize nxtask + // initialize nxtask nxtask_init(rtdb); -//!! BGJ + //!! BGJ bgj_rtdb = rtdb; -//!! BGJ + //!! BGJ if (ostartup || ocontinue){ @@ -308,14 +310,14 @@ int main(){ nw_print_restart_info(rtdb); } -// if continue then go right to task stored on rtdb do not further parse -// input. if input is required then user should have used restart + // if continue then go right to task stored on rtdb do not further parse + // input. if input is required then user should have used restart if (ocontinue){ task(rtdb); } -// Parse input data, shove into database and execute tasks + // Parse input data, shove into database and execute tasks g10 if (input_parse(rtdb)){ // while(tasks to do) util_print_rtdb_load(rtdb, ' '); // High level print @@ -332,7 +334,7 @@ int main(){ goto g10; // end while } -// Close the RTDB + // Close the RTDB util_print_rtdb_load(rtdb, ' '); // High level print if (util_print('rtdbvalues', print_debug)){ @@ -353,15 +355,15 @@ int main(){ rtdb_print_usage(); // Called after closing so memory leaks apparent } -// Tidy up pstat + // Tidy up pstat if (!pstat_terminate()){ errquit('nwchem: pstat_terminate failed', 0, UNKNOWN_ERR); } -//** nxtval_ga_terminate() + //** nxtval_ga_terminate() -// Print memory and other info + // Print memory and other info ga_sync(); if (ga_nodeid == 0){ @@ -401,3 +403,148 @@ int main(){ return 0; } + + +/* +void nwchem_head_info(char* argv[]) { + + int ierr, num_procs, nodeid; + + ierr = MPI_Init(&argc, &argv); + + ierr = MPI_Comm_rank(MPI_COMM_WORLD, &nodeid); + ierr = MPI_Comm_size(MPI_COMM_WORLD, &num_procs); + + ierr = MPI_Finalize(); + + + + FILE *fptr; + time_t timer; + struct tm* tm_info; + + char compiled[] = __TIMESTAMP__; + char nwchem_rev[] = VERSION; + char branch[] = NWCHEM_BRANCH; + char *raw_srcdir = realpath(argv[0], NULL); + + char c, hostname[80], executable[nw_max_path_len], date[26], input_filename[nw_max_path_len]; + char ga_rev[nw_max_path_len], srcdir[nw_max_path_len], thing[32][nw_max_path_len], *ptr; + char rtdb_name[nw_max_path_len], file_prefix[nw_max_path_len], folder_prefix[nw_max_path_len]; + char cstart[10]; + int host_return, i, depth, nproc; + + strncpy(input_filename, argv[1], nw_max_path_len-1); + + printf(" argument 1 = %s\n\n", input_filename); + // printf("%.*s", 30, "================="); + //printf("%0*d\n", 20, 0); + printf("\n\n=============================="); + printf(" echo of input deck "); + printf("==============================\n"); + + // Open file + fptr = fopen(input_filename, "r"); + if (fptr == NULL) + { + printf("Cannot open file \n"); + exit(0); + } + + // Read contents from file + c = fgetc(fptr); + while (c != EOF) + { + printf("%c", c); + c = fgetc(fptr); + } + + // Close file + fclose(fptr); + + printf("\n=========================================="); + printf("======================================\n\n\n\n\n\n\n"); + + // Printing hostname + host_return = gethostname(hostname, sizeof(hostname)); + if (host_return == -1) errquit("nwchem: failed to get hostname", 0, 10); + + // Printing program + strncpy(executable, argv[0], nw_max_path_len-1); + + // Printing current date + timer = time(NULL); + tm_info = localtime(&timer); + strftime(date, 30, "%a %b %d %H:%M:%S %Y", tm_info); + + // Reformatting compilation date + ptr = compiled; + while (*ptr) { + if (*ptr == ' ') + *ptr = '_'; + ptr++; + } + + // Getting top-level source folder + depth = 0; + ptr = strtok(raw_srcdir, "/"); + while (ptr != NULL) { + strcpy(thing[depth], ptr); + ptr = strtok(NULL, "/"); + depth++; + } + + depth -= 3; + i = 0; + srcdir[0] = '\0'; + while (i < depth) { + strcat(srcdir, "/"); + strcat(srcdir, thing[i+1]); + i++; + } + + // Getting release info (OLD) +/*#ifdef RELEASE + #define NWCHEM_BRANCH "7.0.2" +#else + #define NWCHEM_BRANCH "Development" +#endif/* + + // Printing GA info + strncpy(ga_rev, "5.7.2", 79); + + snprintf(file_prefix, 79, "%s.", "eu_hdehp_cmpx"); + + strncpy(folder_prefix, "./perm", nw_max_path_len-2); + snprintf(rtdb_name, nw_max_path_len, "%s/%sdb", folder_prefix, file_prefix); + + strncpy(cstart, "startup", 9); + +#if defined(MPI) + MPI_Comm_size(MPI_COMM_WORLD, &nproc); +#elif defined(_OPENMP) + nproc = omp_get_num_threads(); +#else + nproc = 1; +#endif + + printf(" Job information\n"); + printf(" ---------------\n"); + printf(" hostname = %s\n", hostname); + printf(" program = %s\n", executable); + printf(" date = %s\n\n", date); + + printf(" compiled = %s\n", compiled); + printf(" source = %s\n", srcdir); + printf(" nwchem branch = %s\n", branch); + printf(" nwchem revision = %s\n", nwchem_rev); + printf(" ga revision = %s\n", ga_rev); + printf(" use scalapack = %s\n", util_scalapack_info() ? "T" : "F"); + printf(" input = %s\n", input_filename); + printf(" prefix = %s\n", file_prefix); + printf(" data base = %s\n", rtdb_name); + printf(" status = %s\n", cstart); + printf(" nproc = %8d\n", nproc); + printf(" time left = %6ds\n", util_batch_job_time_remaining()); +*/ + diff --git a/src/rtdb/Makefile b/src/rtdb/Makefile new file mode 100644 index 0000000..64a2a4b --- /dev/null +++ b/src/rtdb/Makefile @@ -0,0 +1,39 @@ + +LIBRARY = libnwcutil.a +LIBRARIES += $(LIBRARY) + +OBJ_OPTIMIZE += rtdb.o rtdb_seq.o context.o + +HEADERS = context.h rtdb.h rtdb.cray.h + +LIB_TARGETS = test test.o rtdbtest rtdbtest.o interact context davetest \ + context.o davetest.o interact.o rtdb_par_f2c.o \ + cntx.o cntx testgr.o testgr + +TEST_LIBS = $(LIBRARY) $(LIBS) + +$(LIBRARY): $(LIB_TARGETS) + +davetest: davetest.o $(LIBRARY_PATH) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ davetest.o $(LIBS) + +cntx: cntx.o $(LIBRARY_PATH) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + +interact: interact.o $(LIBRARY_PATH) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ interact.o $(LIBRARY_PATH) -lglobal -ltcgmsg -lm + +test: test.o $(LIBRARY_PATH) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + +testgr: testgr.o $(LIBRARY_PATH) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + +rtdbtest: rtdbtest.o $(LIBRARY_PATH) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lm $(LIBS) + +rtdbpartest: rtdb_par_test.o $(LIBRARY) + $(CC) $(CFLAGS) -o $@ rtdb_par_test.o $(TEST_LIBS) + +context: context.o $(LIBRARY) + $(CC) $(CFLAGS) -o $@ context.o $(TEST_LIBS) \ No newline at end of file diff --git a/src/rtdb/context.c b/src/rtdb/context.c new file mode 100644 index 0000000..157b5d9 --- /dev/null +++ b/src/rtdb/context.c @@ -0,0 +1,210 @@ +/*$Id$*/ +#include +#include +#include +#include "rtdb.h" +#include "macdecls.h" +#include "misc.h" + +#define MAX_CLEN 4096 +static char context[MAX_CLEN]; + +int context_set(const char *string) +{ + if (strlen(string) < sizeof(context)) { + (void) strcpy(context, string); + return 1; + } + else { + fprintf(stderr, "context_set: string too long? %s\n", string); + fflush(stderr); + return 0; + } +} + +char *context_get(void) +{ + return strdup(context); +} + +int context_rtdb_store(int rtdb) +{ + return rtdb_put(rtdb, "Context", MT_CHAR, strlen(context)+1, context); +} + +int context_rtdb_load(int rtdb) +{ + return rtdb_get(rtdb, "Context", MT_CHAR, sizeof(context), context); +} + +int context_push(const char *string) +{ + int clen = strlen(context); + int slen = strlen(string); + + if (slen+clen+2 >= sizeof(context)) { + fprintf(stderr, "context_push: static dimension of context too small\n"); + fprintf(stderr, "context_push: current = %s\n", context); + fprintf(stderr, "context_push: pushing = %s\n", string); + return 0; + } + else { + (void) strcpy(context+clen, string); + (void) strcpy(context+clen+slen, ":"); + return 1; + } +} + +int context_pop(const char *string) +{ + int clen = strlen(context); + int slen = strlen(string); + + if (clen) + clen--; /* Trailing colon */ + + if (slen <= clen && strncmp(context+clen-slen, string, slen) == 0) { + context[clen-slen] = 0; + return 1; + } + else { + fprintf(stderr, "context_pop: current = %s\n", context); + fprintf(stderr, "context_pop: popping = %s\n", string); + return 0; + } +} + +int context_rtdb_match(int rtdb, const char *name, int reslen, + char *result) +{ + char buf[MAX_CLEN]; + int blen = strlen(context); + + if (blen+strlen(name)+1 > sizeof(buf)) { + fprintf(stderr, "context_rtdb_match: buffer size exceeded\n"); + fprintf(stderr, "context_rtdb_match: current = %s\n", context); + fprintf(stderr, "context_rtdb_match: pushing = %s\n", name); + return 0; + } + + strcpy(buf, context); + + while (1) { + int ma_type, nelem; + char date[26]; + + /* Append name to current context */ + + (void) strcpy(buf+blen, name); + + if (rtdb_get_info(rtdb, buf, &ma_type, &nelem, date)) { + if (ma_type == MT_CHAR) { + if (!rtdb_get(rtdb, buf, ma_type, reslen, result)) { + fprintf(stderr, "context_rtdb_match: rtdb_get failed?\n"); + return 0; + } + reslen = strlen(result); + if (result[reslen-1] == '\n') /* Fortran cput appends an unwanted CR */ + result[reslen-1] = 0; + return 1; + } + else { + fprintf(stderr, "context_rtdb_match: found %s but is wrong type\n", + name); + return 0; + } + } + else { + + /* Did not find entry ... pop the context stack */ + + if (!blen) + return 0; /* Stack is alredy empty */ + + blen--; + while (--blen > 0) + if (buf[blen] == ':') + break; + } + } + + return 1; /* Never executed */ +} + + + +int context_prefix(const char *name, char *result, int result_len) +{ + if ((strlen(name)+strlen(context)+1) > result_len) { + fprintf(stderr, "constant_prefix: result too short\n"); + return 0; + } + strcpy(result,context); + strcpy(result+strlen(context),name); + + return 1; +} + +/* +static void context_print() +{ + printf("context = -%s-\n", context); +} +int main() +{ + int rtdb; + char *cntx; + + (void) MA_initialize(MT_CHAR, -1, -1); + + if (!rtdb_open("test.db", "unknown", &rtdb)) + error("testcontext: open failed on %s\n", "test.db"); + + context_print(); + if (!context_push("optimize")) + error("context push failed %d\n", 0); + context_print(); + if (!context_push("scf")) + error("context push failed %d\n", 0); + context_print(); + if (!context_push("rhf")) + error("context push failed %d\n", 0); + context_print(); + if (!context_push("pcg")) + error("context push failed %d\n", 0); + context_print(); + + (void) context_store(rtdb); + + (void) context_set(""); + + (void) context_print(); + + if (!context_load(rtdb)) + error("context_load: failed %d\n", 0); + + (void) context_print(); + + cntx = context_get(); + printf("context from get = %s\n", cntx); + + if (context_pop("scf")) + error("context pop succeeded %d\n", 0); + if (!context_pop("pcg")) + error("context pop failed %d\n", 0); + context_print(); + if (!context_pop("rhf")) + error("context pop failed %d\n", 0); + context_print(); + if (!context_pop("scf")) + error("context pop failed %d\n", 0); + context_print(); + if (!context_pop("optimize")) + error("context pop failed %d\n", 0); + context_print(); + + (void) rtdb_close(rtdb, "delete"); + + return 0; +} +*/ \ No newline at end of file diff --git a/src/rtdb/context.h b/src/rtdb/context.h new file mode 100644 index 0000000..1dc297e --- /dev/null +++ b/src/rtdb/context.h @@ -0,0 +1,14 @@ +/*$Id$*/ +int context_set(const char *); +char *context_get(void); +int context_rtdb_store(int); +int context_rtdb_load(int); +int context_push(const char *); +int context_pop(const char *); +int context_rtdb_match(int, const char *, int, char *); +int context_prefix(const char *, char *, int); + + +#if defined(CRAY) || defined(WIN32) +#include "rtdb.cray.h" +#endif \ No newline at end of file diff --git a/src/rtdb/davetest.c b/src/rtdb/davetest.c new file mode 100644 index 0000000..7d83412 --- /dev/null +++ b/src/rtdb/davetest.c @@ -0,0 +1,15 @@ + + +int main(int argc, char *argv[]) { + + char name[128]; + int rtdb; + int crap; + + strncpy(name, "h2o.db", 12); + + pbeinf(); + + + return 0; +} \ No newline at end of file diff --git a/src/rtdb/rtdb.cray.h b/src/rtdb/rtdb.cray.h new file mode 100644 index 0000000..9a211e9 --- /dev/null +++ b/src/rtdb/rtdb.cray.h @@ -0,0 +1,26 @@ + +/*$Id$*/ +#if (defined(CRAY) || defined(WIN32)) &&!defined(__crayx1) &&!defined(__MINGW32__) +#define context_pop_ CONTEXT_POP +#define context_prefix_ CONTEXT_PREFIX +#define context_push_ CONTEXT_PUSH +#define context_rtdb_load_ CONTEXT_RTDB_LOAD +#define context_rtdb_match_ CONTEXT_RTDB_MATCH +#define context_rtdb_store_ CONTEXT_RTDB_STORE +#define context_set_ CONTEXT_SET +#define context_get_ CONTEXT_GET +#define rtdb_cget_ RTDB_CGET +#define rtdb_close_ RTDB_CLOSE +#define rtdb_cput_ RTDB_CPUT +#define rtdb_delete_ RTDB_DELETE +#define rtdb_first_ RTDB_FIRST +#define rtdb_get_ RTDB_GET +#define rtdb_get_info_ RTDB_GET_INFO +#define rtdb_ma_get_ RTDB_MA_GET +#define rtdb_next_ RTDB_NEXT +#define rtdb_open_ RTDB_OPEN +#define rtdb_parallel_ RTDB_PARALLEL +#define rtdb_put_ RTDB_PUT +#define rtdb_print_ RTDB_PRINT +#define rtdb_print_usage_ RTDB_PRINT_USAGE +#endif \ No newline at end of file diff --git a/src/rtdb/testgr.c b/src/rtdb/testgr.c new file mode 100644 index 0000000..58f1b4b --- /dev/null +++ b/src/rtdb/testgr.c @@ -0,0 +1,32 @@ +#include + +#include "rtdb.h" + + +int main(int argc, char *argv[]) { + + int rtdb, ma_handle, ma_index; + int itest[3], ibuf[3]; + float ftest[4], fbuf[4]; + double dtest[5], dbuf[5]; + char cbuf[4][20], ccbuf[4][20]; + char name[20], rtdb_fname[20]; + char date[26]; + bool status; + int type, nelem, i; + + itest = {1, 2, 3}; + ftest = {1.0, 2.0, 3.0, 4.0}; + dtest = {1.0, 2.0, 3.0, 4.0, 5.0}; + + cbuf[0] = "Have"; + cbuf[1] = "a"; + cbuf[2] = "nice"; + cbuf[3] = "day, Robert!"; + + pbeginf(); + if (!ma_init(MT_DBL, -1, -1)) exit; + ga_initialize() + + +} \ No newline at end of file diff --git a/src/util/global.h b/src/util/global.h new file mode 100644 index 0000000..400ff13 --- /dev/null +++ b/src/util/global.h @@ -0,0 +1,11 @@ +#ifndef _GLOBAL_H +#define _GLOBAL_H + +const int MT_DBL = 8; +const int MT_INT = 4; + +int nodeid(); + +double *dbl_mb; + +#endif \ No newline at end of file diff --git a/src/util/printlevels.h b/src/util/printlevels.h new file mode 100644 index 0000000..022270a --- /dev/null +++ b/src/util/printlevels.h @@ -0,0 +1,12 @@ +#ifndef _PRINTLEVELS_H +#define _PRINTLEVELS_H + + const int print_none = 0; + const int print_low = 10; + const int print_medium = 20; + const int print_high = 30; + const int print_debug = 100; + const int print_default = print_medium; + const int print_never = 1000000; + +#endif \ No newline at end of file diff --git a/src/util/stdio.h b/src/util/stdio.h new file mode 100644 index 0000000..5c948b4 --- /dev/null +++ b/src/util/stdio.h @@ -0,0 +1,56 @@ +#ifndef _USER_STDIO_H +#define _USER_STDIO_H +//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: +// NAME +// stdio -- define logical units for standard I/O +// +// REVISION +// $Id$ +// +// NOTES +// The common block must be initialized prior to using the I/O +// units. Currently the following points change these units: +// +// 1) Block data util_stdio_data [util_io.F] sets LuOut to 6 as a +// sensible default. +// +// 2) Function util_sgroup_set_ioname [util_sgroup.F] sets LuOut +// to a value based on the group number. +// +// 3) Function util_sgroup_unset_io [util_sgroup.F] closes LuOut. +// +// 4) Subroutine smd_group_set_io [smd_group.F] closes LuOut, +// resets it, and attaches it to a new file. +// +// 5) Subroutine smd_group_set_io_custom [smd_group.F] closes LuOut, +// resets it, and attaches it to a new file. +// +// 6) Subroutine smd_group_unset_io [smd_group.F] closes LuOut. +// +// This combination ensures that subgroup aware codes can arrange +// the I/O capabilities they need, while functionality that is +// not subgroup aware still works because of a proper default +// setting. +//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: +// +// This way we do not have to worry about the +// initialization/termination +// + + char LuOut[511]; + +#endif +// +// A potentially useful tidbit: On Cray machines, units +// 100, 101, and 102 are always assigned to stdin, stdout, and +// stderr. They differ from 5, 6, and 0 in that they cannot be +// OPENed, and will not exist according to INQUIRE. Consequently, +// 100+ will _always_ correspond to the unix stdio streams regardless +// of what the application may do with 5/6/0 +// +// Also note that on Crays, all of these units are _assigned_ but not +// preconnected. That means if you try to call something like flush +// on a unit that you have not written to previously (implicitly +// opeining it), it causes a fatal error. + +#endif \ No newline at end of file diff --git a/src/util/util.h b/src/util/util.h new file mode 100644 index 0000000..a7792aa --- /dev/null +++ b/src/util/util.h @@ -0,0 +1,11 @@ +#ifndef _UTIL_H +#define _UTIL_H + + #include + #include "printlevels.h" + #include "util_maxlength.h" + + const int nw_max_path_len = 255; // Maximum path len -> posix standard is what? + const int nw_max_path_len = MAXLENGTH; // Maximum path len -> posix standard is what? + +#endif \ No newline at end of file From ad310f6e65f91ea273f97005c7e38505117b11d6 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Wed, 10 Jan 2024 11:44:35 -0800 Subject: [PATCH 09/11] Initial commit. Basic ignore files. --- .gitignore | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..c36ea02 --- /dev/null +++ b/.gitignore @@ -0,0 +1,10 @@ +.vscode +bin/ +build/ + +.DS_Store + +*.a +*.lo +*.o +*.so \ No newline at end of file From ec4e4388fe43695c1a7244ba745213797f1f4015 Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Fri, 19 Jan 2024 15:38:35 -0800 Subject: [PATCH 10/11] some basic files --- src/basis/GNUmakefile | 15 + src/basis/bas.h | 38 + src/basis/basP.h | 194 +++++ src/basis/bas_input.c | 273 +++++++ src/basis/bas_staticP.h | 14 + src/basis/basdeclsP.h | 39 + src/basis/basis.c | 1410 ++++++++++++++++++++++++++++++++++++ src/basis/doc/api | 138 ++++ src/basis/doc/basis.doc | 149 ++++ src/basis/doc/basis.output | 139 ++++ src/basis/doc/robert.doc | 218 ++++++ src/basis/geobasmapP.h | 29 + src/basis/newbasis.c | 11 + src/basis/testbasis.c | 170 +++++ src/config/makefile.h | 176 +++++ src/config/makelib.h | 59 ++ src/geom/GNUmakefile | 9 + src/geom/geom.c | 683 +++++++++++++++++ src/geom/geom.doc | 113 +++ src/geom/geom.h | 31 + src/geom/geomP.h | 84 +++ src/geom/geom_input.c | 98 +++ src/include/GNUmakefile | 20 + src/inp/GNUmakefile | 13 + src/inp/inp.doc | 191 +++++ src/inp/inp.h | 18 + src/inp/inpP.h | 34 + src/inp/test.c | 36 + src/rtdb/GNUmakefile | 47 ++ src/rtdb/context.h | 15 + src/rtdb/rtdb.h | 154 ++++ 31 files changed, 4618 insertions(+) create mode 100644 src/basis/GNUmakefile create mode 100644 src/basis/bas.h create mode 100644 src/basis/basP.h create mode 100644 src/basis/bas_input.c create mode 100644 src/basis/bas_staticP.h create mode 100644 src/basis/basdeclsP.h create mode 100644 src/basis/basis.c create mode 100644 src/basis/doc/api create mode 100644 src/basis/doc/basis.doc create mode 100755 src/basis/doc/basis.output create mode 100644 src/basis/doc/robert.doc create mode 100644 src/basis/geobasmapP.h create mode 100644 src/basis/newbasis.c create mode 100644 src/basis/testbasis.c create mode 100644 src/config/makefile.h create mode 100644 src/config/makelib.h create mode 100644 src/geom/GNUmakefile create mode 100644 src/geom/geom.c create mode 100644 src/geom/geom.doc create mode 100644 src/geom/geom.h create mode 100644 src/geom/geomP.h create mode 100644 src/geom/geom_input.c create mode 100644 src/include/GNUmakefile create mode 100644 src/inp/GNUmakefile create mode 100644 src/inp/inp.doc create mode 100644 src/inp/inp.h create mode 100644 src/inp/inpP.h create mode 100644 src/inp/test.c create mode 100644 src/rtdb/GNUmakefile create mode 100644 src/rtdb/context.h create mode 100644 src/rtdb/rtdb.h diff --git a/src/basis/GNUmakefile b/src/basis/GNUmakefile new file mode 100644 index 0000000..b5fb2df --- /dev/null +++ b/src/basis/GNUmakefile @@ -0,0 +1,15 @@ + HEADERS = bas.h basP.h bas_staticP.h + OBJ = basis.o newbasis.o bas_input.o + LIBRARY = libbasis.a + LIB_TARGETS = testbasis testbasis.o + +include ../config/makefile.h +include ../config/makelib.h + +testbasis: testbasis.o $(LIBRARY) + $(FC) $(FFLAGS) -o $@ testbasis.o $(LIBS) + + +basis.o: basP.h geobasmapP.h basdeclsP.h +basP.h: bas_staticP.h + @touch basP.h \ No newline at end of file diff --git a/src/basis/bas.h b/src/basis/bas.h new file mode 100644 index 0000000..7bb6cfd --- /dev/null +++ b/src/basis/bas.h @@ -0,0 +1,38 @@ +#ifndef _BAS_H +#define _BAS_H + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +void bas_input(FILE *rtdb); +void bas_input_body(int basis, bool osegment); +bool gbs_map_clear(int basisin); + + bool bas_create(); + bool bas_destroy(); + bool bas_check_handle(int basisin, char *msg); + bool bas_321g_load(); + bool bas_print(); + bool bas_rtdb_load(); + bool bas_rtdb_store(); + bool bas_high_angular(); + bool gbs_map_print(); + bool bas_continfo(); + bool bas_numcont(); + bool bas_numbf(); + bool bas_get_exponent(); + bool bas_get_coeff(); + bool bas_set_exponent(); + bool bas_set_coeff(); + bool bas_print_all(); + bool bas_version(); + void bas_add_ucnt(int, char *, int, int, int, double*, double*, int); + +#ifdef __cplusplus +} +#endif + +#endif // _BAS_H_ diff --git a/src/basis/basP.h b/src/basis/basP.h new file mode 100644 index 0000000..196d8dd --- /dev/null +++ b/src/basis/basP.h @@ -0,0 +1,194 @@ +#ifndef _BASP_H +#define _BASP_H + +/* + basis set object/api + Rick A. Kendall and Robert J. Harrison (March 1994) + + What is the minimum basis set informaton? + + What is a basis set? A basis set is a set of tags nominally + associated with an atomic center through a geometry specification + or geometry object. What needs to be stored is the basis set for + the unique tags ("atoms"). The concept of shell and general + contraction confuses the issue somewhat but in the limit of a + segmented basis set the "shell" concept is the same as the + "general contraction." The basis set object and its interaction + with the integral API is predicated upon this assumption. + + A pseudo input deck with the minimum information is as follows. + Basis Set: Name (as on the rtdb) + ntags (number of unique tags for which basis set + information is supplied) + nucont (total number of unique contractions in basis) + nprim_t (total number of primitives in basis) + ncoef_t (total number of coeffs in basis) + foreach tag (ntags of them) + tag (character string identifier of tag) + number_of_contractions on tag + nprim_c in contractions on tag + ncoeff in contractions on tag + first contraction of tag + last contraction of tag + foreach contraction (number_of_contractions of them) + itype, nprim, ngen, iexptr, icoeff, tag_cont_is_on + foreach nprim in a contraction + ex(1), coeff(1,...) (ngen contractions) + + The tag ("atomic") information pseudo-data structure is as follows: + Integer num_cont ! Number of contractions on tag + Integer nprim_tag ! Number of primitive exponents on tag + Integer ncoeff_tag ! Number of primitive coeffs on tag + Integer ifirst_cont ! first contraction on tag + Integer ilast_cont ! last contraction on tag + Integer itype(num_cont) ! type of contraction 0=s,1=p,2=d... + ! later -1=sp,-2=spd etc. + Integer nprim(num_cont) ! number of primitives in each cont. on tag + Integer ngen(num_cont) ! number of general conts in each cont. + ! 1= segmented basis, >1 general cont. + Integer iexpt(num_cont) ! pointer into linearized real*8 array for + ! first exponent + Integer icoeffpt(num_cont) ! pointer into linearized real*8 array for + ! first coefficient + Integer itag(num_cont) ! tag identifier for contraction + ! (redundant for just atomic info) + double exndcf[nprim_tag+ncoeff_tag] ! linearized real*8 array of + ! exponents and coefficients + + The basis set information is the number of tags and the above tag + information. + + unique information only!!!!!!! + + The basis set information pseudo-data structure is as follows: + char bs_name[256] ! (as "mo basis") + int num_tags ! number of tags in basis + int num_cont_total ! number of conts in basis + int num_prim_total ! number of prims in basis + int num_coeff_total ! number of coefs in basis + char tags[num_tags][16] ! character string of tags + int num_cont[num_tags] ! Num of conts on tag + int nprim_tag[num_tags] ! Num of prim exponents on tag + int ncoeff_tag[num_tags] ! Num of prim coeffs on tag + int itype[num_cont] ! type of contraction 0=s,1=p,2=d... + ! later -1=sp,-2=spd etc. + int nprim[num_cont] ! num of prims in each cont. on tag + int ngen[num_cont] ! num of general conts in each cont. + ! on each tag + ! 1= segmented basis, >1 general cont. + int iexpt[num_cont] ! pointer into linearized real*8 array + ! for first exponent of each cont. + ! on each tag + int icoeffpt[num_cont] ! pointer into linearized real*8 + ! array for first coefficient of + ! each cont. on each tag + int itag[num_cont] ! tag identifier for contraction + ! (redundant for just atomic info) + double exndcf[] ! linearized real*8 array of + ! exponents and coefficients + Note: exndcf does not carry the num_cont label because it is a + linearized real*8 array and the added dimensionality is + handled by proper evaluation of the pointer arrays + iexpt and icoeffpt. + + The above data structure is too cumbersome to efficiently store to + and read from the run-time-data-base (one call per array). The + integer and real*8 data needs to be linearized with appropriate + informaton accessable by pointers arrays. + + The more appropriate "basis" data structure is as follows: + char bs_name[256] ! as "mo basis" + char tags[num_tags][16] ! character string of tags + int infbs_head[4] ! header information + ! 1 = num_tags ! num of tags in basis + ! 2 = num_cont_total ! num of conts in basis + ! 3 = num_prim_total ! num of prims(ex) in basis + ! 4 = num_coeff_total ! num of coeffs in basis + int infbs_tags[5][num_tags] + ! 1 = num_cont ! Num of conts on tag + ! 2 = nprim_tag ! Num of prim exponents on tag + ! 3 = ncoeff_tag ! Num of prim coeffs on tag + ! 4 = first cont ! first contaction on tag + ! 5 = last cont ! last contaction on tag + int infbs_cont[6][num_cont] + ! 1 = itype ! type of contraction 0=s,1=p,2=d... + ! later -1=sp,-2=spd etc. + ! 2 = nprim ! num of prims in each cont. on tag + ! 3 = ngen ! num of general conts in each cont. + ! on each tag + ! 1= segmented basis, >1 general cont. + ! 4 = iexpt ! pointer into linearized real*8 array + ! for first exponent of each cont. + ! on each tag + ! 5 = icoeffpt ! pointer into linearized real*8 + ! array for first coefficient of + ! each cont. on each tag + ! 6 = itag ! cunique tag number + double exndcf[] ! linearized real*8 array of + ! exponents and coefficients + + The above data structure now must handle multiple basis sets. + The "multiple basis set" data structure is as follows: + char bs_name[nbasis][256] ! as "mo basis" + char tags[num_tags][nbasis][16] ! character string of tags + int infbs_head[4][nbasis] + ! 1 = num_tags ! num of tags in basis + ! 2 = num_cont_total ! num of conts in basis + ! 3 = num_prim_total ! num of prims(ex) in basis + ! 4 = num_coeff_total ! num of coeffs in basis + int infbs_tags[5][num_tags][nbasis] + ! 1 = num_cont_tag ! Num of conts on tag + ! 2 = nprim_tag ! Num of prim exponents on tag + ! 3 = ncoeff_tag ! Num of prim coeffs on tag + ! 4 = first cont ! first contraction on tag + ! 5 = last cont ! last contraction on tag + int infbs_cont[6][num_cont_total][nbasis] + ! 1 = itype ! type of contraction 0=s,1=p,2=d... + ! later -1=sp,-2=spd etc. + ! 2 = nprim ! num of prims in each cont. on tag + ! 3 = ngen ! num of general conts in each cont. + ! on each tag + ! 1= segmented basis, >1 general cont. + ! 4 = iexpt ! pointer into linearized real*8 array + ! for first exponent of each cont. + ! on each tag + ! 5 = icoeffpt ! pointer into linearized real*8 + ! array for first coefficient of + ! each cont. on each tag + ! 6 = tag number ! unique center lexical index + double exndcf[][nbasis] ! linearized real*8 array of + ! exponents and coefficients + + actual names are set to protect name space between the geom and + basis objects +*/ +#define BASIS_HANDLE_OFFSET ((0-565)) + +// static dimension information for common blocks +#include "bas_staticP.h" + +// leading dimensions of compressed arrays +#define ndbs_tags 5 +#define ndbs_ucont 6 +#define ndbs_head 4 + +// stored structures +char bs_name[nbasis_bsmx][256]; +char bs_tags[ntags_bsmx][nbasis_bsmx][16]; +double exndcf[mxbs_exndcf][nbasis_bsmx]; +int infbs_head[ndbs_head][nbasis_bsmx]; +int infbs_tags[ndbs_tags][ntags_bsmx][nbasis_bsmx]; +int infbs_cont[ndbs_ucont][nucont_bsmx][nbasis_bsmx]; + +// in-core structures +double bsversion; +char bs_trans[nbasis_bsmx]; +char bs_names_rtdb[nbasis_rtdb_mx][256]; +int len_bs_name[nbasis_bsmx]; +int len_bs_trans[nbasis_bsmx]; +int len_bs_rtdb[nbasis_rtdb_mx]; +int nbasis_rtdb; +int angular_bs[nbasis_bsmx]; +bool bsactive[nbasis_bsmx]; + +#endif // _BASP_H diff --git a/src/basis/bas_input.c b/src/basis/bas_input.c new file mode 100644 index 0000000..4892d93 --- /dev/null +++ b/src/basis/bas_input.c @@ -0,0 +1,273 @@ +#include +#include + +#include "rtdb.h" +#include "context.h" +#include "geom.h" +#include "bas.h" +#include "inp.h" + +void bas_input(FILE *rtdb) { + /* + basis [] [library ] [file ] \ + [spherical|cartesian] [segment] [print] + + tag library [file ] + tag + + ... + end basis + + parse the main directive + */ + + int nopt = 6; + char opts[6][10] = {"spherical", "cartesian", "segment", "library", "file", "print"}; + char test[255], name[255], filename[255], standard[255]; + bool status, ospherical, osegment, oprint; + int ind, basis; + for (int i = 0; i < nopt; i++) { + opts[i][9] = '\0'; + } + + // Check is a basis directive and read in name of the basis + inp_set_field(0); + status = inp_a(test); + if ((!status) || (!inp_compare(false, test, "basis"))) { + goto L10000; + } + + // Parse rest of basis directive line + name[0] = '\0'; + filename[0] = '\0'; + test[0] = '\0'; + standard[0] = '\0'; + ospherical = false; + osegment = false; + oprint = false; + +L10: + if (inp_a(test)) { + if (!inp_match(nopt, false, test, opts, ind)) { + // Not a recognized option ... the name of the basis or an error + if ((name[0] != '\0') || (inp_cur_field() != 2)) { + printf(" bas_input: basis name must be first option\n"); + goto L10000; + } + strcpy(name, test); + goto L10; + } + switch (ind) { + case 0: // spherical + ospherical = true; + goto L10; + case 1: // cartesian + ospherical = false; + goto L10; + case 2: // segment + osegment = true; + goto L10; + case 3: // library + if (!inp_a(standard)) { + goto L10000; + } + goto L10; + case 4: // file + if (!inp_a(filename)) { + goto L10000; + } + goto L10; + case 5: // print + oprint = true; + goto L10; + } + } + + // Now check reality against input + if (standard[0] != '\0') { + printf(" Standard basis %s\n", standard); + errquit("bas_input: standard basis set not yet", 0); + } + if (ospherical) { + errquit("bas_input: spherical harmonics not yet", 0); + } + + // Open a new basis set to receive the new data + if (name[0] == '\0') { + strcpy(name, "mo basis"); + } + if (!bas_create(basis, name)) { + errquit("bas_input: failed to create basis", 0); + } + + // Here will soon process reading standard basis sets + + // Now left with reading in from the input additional specifications + // for basis functions or standard sets on specific tags + bas_input_body(basis, osegment); + + // Now have processed the entire basis directive. Print out + // info if desired, write it to the data base, tidy up and go home + if (oprint) { + if (!bas_print(basis)) { + errquit("bas_input: print failed", 0); + } + } + + if (!bas_rtdb_store(rtdb, name, basis)) { + errquit("bas_input: failed to store basis", 0); + } + + if (!bas_destroy(basis)) { + errquit("bas_input: bas_destroy failed", 0); + } + + return; + +L10000: + printf(" basis [] [library ] \\\n"); + printf(" [file ] [spherical|cartesian] [segment]\n"); + errquit("bas_input: invalid format for basis directive", 0); +} + +void bas_input_body(int basis, bool osegment) { +/* + +c Read the body of a basis directive that describes the +c tags/exponents/contraction coefficients +c +c +c tag library [file ] +c tag +c +c ... +c end basis +*/ + char tag[16], cont_type[16]; + int nltypes = 7, nsptypes = 2, nopts = 2; + int cont_max = 20, prim_max = 20; + double expnt[20], coeff[20][20]; + char ltypes[7] = {'s', 'p', 'd', 'f', 'g', 'h', 'i'}; + char sptypes[2] = {'sp', 'l'}; + int spvalues[2] = {-1, -1}; + char opts[2][8] = {"library", "file"}; + int spvalues[2] = {-1, -1}; + int l_value, ngen, iprim, nprim, i, ind; + +// Input a new line +L10: + if (!inp_read()) { + errquit("bas_input_body: premature EOF", 0); + } + +// Start parsing current line +L20: + inp_set_field(0); + if (!inp_a(tag)) { + goto L10000; + } + + if (inp_compare(false, "end", tag)) { + goto L9000; // End of basis directive + } + + if (!inp_a(cont_type)) { + goto L10000; + } + + if (inp_match(nltypes, false, cont_type, ltypes, ind)) { + // The contraction is a simple shell + l_value = ind - 1; + } else if (inp_match(nsptypes, false, cont_type, sptypes, ind)) { + // The contraction is an sp-type shell + l_value = spvalues[ind]; + } else if (inp_match(nopts, false, cont_type, opts, ind)) { + /* + It is actually an option to input a standard basis + + Don't bother parsing this yet + */ + errquit("bas_input_body: no standard basis sets yet", 0); + goto L10; // Process the next input line + } else { + // Only god and the user knows what was intended + goto L10000; + } + + // Fall thru to here to read in a set of contraction coefficients + if (!inp_read()) { + goto L10000; + } + + ngen = inp_n_field() - 1; + if (ngen < 1) { + goto L10000; + } + if (ngen > cont_max) { + errquit("bas_input_body: too many contractions - increase cont_max", cont_max); + } + + for (iprim = 0; iprim < prim_max; iprim++) { + if (!inp_f(expnt[iprim])) { + // If cannot read the first field as an exponent then + // it is the end of this contraction + + goto L30; + } else { + if ((inp_n_field() - 1) != ngen) { + printf(" bas_input_body: no. of coefficients?\n"); + goto L10000; + } + for (i = 0; i < ngen; i++) { + if (!inp_f(coeff[iprim][i])) { + printf(" bas_input_body: failed reading coefficient\n"); + goto L10000; + } + } + if (!inp_read()) { + goto L10000; + } + } + } + errquit("bas_input_body: too many primitives in contraction", prim_max); + +L30: + nprim = iprim - 1; + if (nprim <= 0) { + errquit("bas_input_body: no primitives?", nprim); + } + + // Now have tag, contraction type, no. of contractions, no. of prims, + // exponents, coeffs. Shove this lot into the basis set. + // bas_add_ucnt -> adds a new general contraction on the specified tag. + // If the tag is not present it will also add that. + if (osegment) { + // Add contractions one-at-a-time to force segmentation + for (i = 0; i < ngen; i++) { + if (!bas_add_ucnt(basis, tag, l_value, 1, nprim, expnt, coeff[0][i], prim_max)) { + errquit("bas_input_body: bas_add_ucnt failed!!", 0); + } + } + } else { + // Add as a single general contraction + if (!bas_add_ucnt(basis, tag, l_value, ngen, nprim, expnt, coeff, prim_max)) { + errquit("bas_input_body: bas_add_ucnt failed!!", 0); + } + } + + // Have already read in the next line ... parse it + goto L20; + +// Have read in all of the basis set info. +L9000: + return; + +L10000: + printf(" basis directive body format is:\n"); + printf(" tag library [file ]\n"); + printf(" tag \n"); + printf(" \n"); + printf(" ... \n"); + printf(" end basis\n"); + errquit("bas_input_body: format error in the input", 0); +} diff --git a/src/basis/bas_staticP.h b/src/basis/bas_staticP.h new file mode 100644 index 0000000..39052a6 --- /dev/null +++ b/src/basis/bas_staticP.h @@ -0,0 +1,14 @@ +#ifndef _BAS_STATICP_H +#define _BAS_STATICP_H + +// Maximum parameter definitions for static "in-core" data structure +const int nbasis_bsmx = 5; +const int nbasis_rtdb_mx = 10 * nbasis_bsmx; +const int ntags_bsmx = 10; +const int nucont_bsmx = 150; +const int mxbs_exndcf = ((300 + 500) * ntags_bsmx); + +const int nat_mx = 1000; +const int ncont_mx = (nucont_bsmx * 4); + +#endif // _BAS_STATICP_H diff --git a/src/basis/basdeclsP.h b/src/basis/basdeclsP.h new file mode 100644 index 0000000..7527fe3 --- /dev/null +++ b/src/basis/basdeclsP.h @@ -0,0 +1,39 @@ +#ifndef _BASDECLSP_H +#define _BASDECLSP_H + +// declarations for substitution by cpp for compressed array count meanings +// only for capitalized versions + +// define HEAD_NTAGS 1 +// define HEAD_NCONT 2 +// define HEAD_NPRIM 3 +// define HEAD_NCOEF 4 +// define TAG_NCONT 1 +// define TAG_NPRIM 2 +// define TAG_NCOEF 3 +// define TAG_FCONT 4 +// define TAG_LCONT 5 +// define CONT_TYPE 1 +// define CONT_NPRIM 2 +// define CONT_NGEN 3 +// define CONT_IEXP 4 +// define CONT_ICFP 5 +// define CONT_TAG 6 + +#define HEAD_NTAGS 1 +#define HEAD_NCONT 2 +#define HEAD_NPRIM 3 +#define HEAD_NCOEF 4 +#define TAG_NCONT 1 +#define TAG_NPRIM 2 +#define TAG_NCOEF 3 +#define TAG_FCONT 4 +#define TAG_LCONT 5 +#define CONT_TYPE 1 +#define CONT_NPRIM 2 +#define CONT_NGEN 3 +#define CONT_IEXP 4 +#define CONT_ICFP 5 +#define CONT_TAG 6 + +#endif \ No newline at end of file diff --git a/src/basis/basis.c b/src/basis/basis.c new file mode 100644 index 0000000..e2fc025 --- /dev/null +++ b/src/basis/basis.c @@ -0,0 +1,1410 @@ +#include +#include +#include + +#include "inp.h" +#include "basP.h" +#include "geom.h" +#include "rtdb.h" +#include "geomP.h" +#include "context.h" +#include "basdeclsP.h" +#include "geobasmapP.h" + +/* + Block data structure to initialize the common block variables in the + internal basis set object data structures +*/ +int nbasis_rtdb = 0; +bool bsactive[nbasis_bsmx] = {false}; // Assuming nbasis_bsmx is a predefined constant +int angular_bs[nbasis_bsmx] = {-565}; // Assuming nbasis_bsmx is a predefined constant +double bsversion = 1.00; + +bool bas_version() { +/* + Routine that calclulates the size of the common block structures + used in the basis set object and the mapped representation object. + input none + output always true. +*/ + int cdata, idata, rdata; + int mapidata, total4, total8; + + // character data + cdata = 256 * 2 * nbasis_bsmx + 256 * nbasis_rtdb_mx; + cdata = cdata + 16 * ntags_bsmx * nbasis_bsmx; + + // real data + rdata = mxbs_exndcf * nbasis_bsmx + 1; + rdata = 8 * rdata; + + // integer data in basis set object common + idata = ndbs_head * nbasis_bsmx; + idata = idata + ndbs_tags * ntags_bsmx * nbasis_bsmx; + idata = idata + ndbs_ucont * nucont_bsmx * nbasis_bsmx; + idata = idata + nbasis_bsmx * 4 + 1; + idata = idata + nbasis_rtdb_mx; + idata = 4 * idata; + + // integer data in the mapped object. + mapidata = 4 * ncont_mx * nbasis_bsmx; + mapidata = mapidata + 3 * nat_mx * nbasis_bsmx; + mapidata = mapidata + 4 * nbasis_bsmx; + mapidata = 4 * mapidata; + + // total space + total4 = idata + mapidata; + total8 = 2 * total4 + rdata + cdata; + total4 = total4 + rdata + cdata; + + printf(" **** basis set version %f ****\n", bsversion); + printf(" character data in-core %d bytes\n", cdata); + printf(" real data in-core %d bytes\n", rdata); + printf(" integer*4 data in-core %d bytes\n", idata); + printf("or integer*8 data in-core %d bytes\n", (2 * idata)); + printf(" integer*4 mapping data in-core %d bytes\n", mapidata); + printf("or integer*8 mapping data in-core %d bytes\n", (2 * mapidata)); + printf(" total(4) = %d bytes\n", total4); + printf(" total(8) = %d bytes\n", total8); + + // convert to kilobytes + cdata = (cdata + 999) / 1000; + rdata = (rdata + 999) / 1000; + idata = (idata + 999) / 1000; + mapidata = (mapidata + 999) / 1000; + total4 = (total4 + 999) / 1000; + total8 = (total8 + 999) / 1000; + + printf(" **** basis set version %f ****\n", bsversion); + printf(" character data in-core %d Kbytes\n", cdata); + printf(" real data in-core %d Kbytes\n", rdata); + printf(" integer*4 data in-core %d Kbytes\n", idata); + printf("or integer*8 data in-core %d Kbytes\n", (2 * idata)); + printf(" integer*4 mapping data in-core %d Kbytes\n", mapidata); + printf("or integer*8 mapping data in-core %d Kbytes\n", (2 * mapidata)); + printf(" total(4) = %d Kbytes\n", total4); + printf(" total(8) = %d Kbytes\n", total8); + + return true; +} + +bool bas_create(FILE *basis, char *name) { +/* + creates a handle and marks it active in the in-core data structure + + passed + integer basis [output] returned handle + char*(*) name [input] name of basis set. +*/ + int i; + + for (i = 0; i <= nbasis_bsmx; i++) { + if (!bsactive[i]) break; + } + + if (i > nbasis_bsmx) { + printf(" bas_create: no free basis handles for %s\n", name); + return false; + } + + // store some information in basis data structure + // (NOTE: name discarded in LOAD operation) + bs_name[basis] = name; + len_bs_name[basis] = strlen(name); + + // Initialize basis info to be empty + bs_trans[basis] = " "; + int *infbs_head[basis] = malloc(ndbs_head * sizeof(int)); + double *exndcf[basis] = malloc(mxbs_exndcf * sizeof(double)); + int *infbs_tags[basis] = malloc(ndbs_tags * ntags_bsmx * sizeof(int)); + int *infbs_cont[basis] = malloc(ndbs_ucont * nucont_bsmx * sizeof(int)); + + // Initialize geo-basis info to empty + int *ibs_cn2ucn[basis] = malloc( ncont_mx * sizeof(int)); + int *ibs_cn2ce[basis] = malloc(ncont_mx * sizeof(int)); + int *ibs_ce2uce[basis] = malloc(nat_mx * sizeof(int)); + int *ibs_cn2bfr[basis] = malloc(2 * ncont_mx * sizeof(int)); + int *ibs_ce2cnr[basis] = malloc(2 * nat_mx * sizeof(int)); + ncont_tot_gb[basis] = 0; + nprim_tot_gb[basis] = 0; + nbf_tot_gb[basis] = 0; + ibs_geom[basis] = 0; + + // Mark basis as active and return info + bsactive[basis] = true; + basis = basis - BASIS_HANDLE_OFFSET; + return true; + +} + +bool bas_destroy(FILE *basisin) { + /* + destroys information about an active incore basis + and the associated mapping arrays. + */ + + bool ret_val; + int basis; + + ret_val = bas_check_handle(basisin, "bas_destroy"); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (!gbs_map_clear(basisin)) { + printf(" error clearing map "); + return false; + } + + bsactive[basis] = false; + + return true; +} + +bool bas_check_handle(FILE *basisin, char *msg) { + + // Checks to see if a basis handle is valid + + // local variables + bool ret_val; + int basis; + basis = basisin + BASIS_HANDLE_OFFSET; + ret_val = (basis > 0 && basis <= nbasis_bsmx); + if (ret_val) { + ret_val = ret_val && bsactive[basis]; + } + + if (!ret_val) { + printf("%s: basis handle is invalid\n", msg); + printf("basis_check_handle: lexical handle %d\n", basis); + printf("basis_check_handle: handle %d\n", basisin); + } + return ret_val; +} + +bool bas_321g_load(FILE *rtdb) { + /* + routine to load the rtdb with 321g basis sets for atoms 1-20 + H to Ca + */ + + // local variables + bool ret_val; + int basis, usebas, itag, icont; + + if (!bas_create(basis, "321g:1-20")) { + printf("basis set handle not created\n"); + return false; + } + + usebas = basis + BASIS_HANDLE_OFFSET; + bs_name[usebas] = "321g:1-20"; + + // only h and o for now + + // hydrogen and oxygen + bs_tags[0][usebas] = 'H'; + bs_tags[1][usebas] = 'He'; + bs_tags[2][usebas] = 'O'; + infbs_head[HEAD_NTAGS][usebas] = 3; + infbs_head[HEAD_NCONT][usebas] = 9; + infbs_head[HEAD_NPRIM][usebas] = 30; + infbs_head[HEAD_NCOEF][usebas] = 30; + + // hydrogen + itag = 0; + infbs_tags[TAG_NCONT][itag][usebas] = 2; + infbs_tags[TAG_NPRIM][itag][usebas] = 3; + infbs_tags[TAG_NCOEF][itag][usebas] = 3; + infbs_tags[TAG_FCONT][itag][usebas] = 1; + infbs_tags[TAG_LCONT][itag][usebas] = 2; + + // hydrogen cont 1 bas 1 + icont = 0; + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 2; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 1; + infbs_cont[CONT_ICFP][icont][usebas] = 3; + infbs_cont[CONT_TAG][icont][usebas] = itag; + exndcf[1][usebas] = 5.44717800; + exndcf[2][usebas] = 0.82454700; + exndcf[3][usebas] = 0.15628500; + exndcf[4][usebas] = 0.90469100; + + // hydrogen cont 2 bas 2 + icont++; + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 1; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 5; + infbs_cont[CONT_ICFP][icont][usebas] = 6; + infbs_cont[CONT_TAG][icont][usebas] = itag; + exndcf[5][usebas] = 0.18319200; + exndcf[6][usebas] = 1.00000000; + + // helium + itag++; + icont++; + infbs_tags[TAG_NCONT][itag][usebas] = 2; + infbs_tags[TAG_NPRIM][itag][usebas] = 3; + infbs_tags[TAG_NCOEF][itag][usebas] = 3; + infbs_tags[TAG_FCONT][itag][usebas] = icont; + infbs_tags[TAG_LCONT][itag][usebas] = icont + 2 - 1; + + // helium cont 1 bas 3 + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 2; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 7; + infbs_cont[CONT_ICFP][icont][usebas] = 9; + infbs_cont[CONT_TAG][icont][usebas] = itag; + exndcf[7][usebas] = 13.62670000; + exndcf[8][usebas] = 1.99935000; + exndcf[9][usebas] = 0.17523000; + exndcf[10][usebas] = 0.89348300; + + // helium cont 2 bas 4 + icont++; + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 1; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 11; + infbs_cont[CONT_ICFP][icont][usebas] = 12; + infbs_cont[CONT_TAG][icont][usebas] = itag; + exndcf[11][usebas] = 0.38299300; + exndcf[12][usebas] = 1.00000000; + + // oxygen + itag++; + icont++; + infbs_tags[TAG_NCONT][itag][usebas] = 5; + infbs_tags[TAG_NPRIM][itag][usebas] = 9; + infbs_tags[TAG_NCOEF][itag][usebas] = 9; + infbs_tags[TAG_FCONT][itag][usebas] = icont; + infbs_tags[TAG_LCONT][itag][usebas] = icont + 5 - 1; + + // oxygen cont 1 bas 5 + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 3; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 13; + infbs_cont[CONT_ICFP][icont][usebas] = 16; + infbs_cont[CONT_TAG][icont][usebas] = itag; + exndcf[13][usebas] = 322.03700000; + exndcf[14][usebas] = 48.43080000; + exndcf[15][usebas] = 10.42060000; + exndcf[16][usebas] = 0.05923940; + exndcf[17][usebas] = 0.35150000; + exndcf[18][usebas] = 0.70765800; + + // oxygen cont 2 bas 6 + icont++; + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 2; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 19; + infbs_cont[CONT_ICFP][icont][usebas] = 21; + infbs_cont[CONT_TAG][icont][usebas] = 2; + exndcf[19][usebas] = 7.40294000; + exndcf[20][usebas] = 1.57620000; + exndcf[21][usebas] = -0.40445300; + exndcf[22][usebas] = 1.22156000; + + // oxygen cont 3 bas 7 + icont++; + infbs_cont[CONT_TYPE][icont][usebas] = 1; + infbs_cont[CONT_NPRIM][icont][usebas] = 2; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 23; + infbs_cont[CONT_ICFP][icont][usebas] = 25; + infbs_cont[CONT_TAG][icont][usebas] = 2; + exndcf[23][usebas] = 7.40294000; + exndcf[24][usebas] = 1.57620000; + exndcf[25][usebas] = 0.24458600; + exndcf[26][usebas] = 0.85395500; + + // oxygen cont 4 bas 8 + icont++; + infbs_cont[CONT_TYPE][icont][usebas] = 0; + infbs_cont[CONT_NPRIM][icont][usebas] = 1; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 27; + infbs_cont[CONT_ICFP][icont][usebas] = 28; + infbs_cont[CONT_TAG][icont][usebas] = 2; + exndcf[27][usebas] = 0.37368400; + exndcf[28][usebas] = 1.00000000; + + // oxygen cont 5 bas 9 + icont++; + infbs_cont[CONT_TYPE][icont][usebas] = 1; + infbs_cont[CONT_NPRIM][icont][usebas] = 1; + infbs_cont[CONT_NGEN][icont][usebas] = 1; + infbs_cont[CONT_IEXP][icont][usebas] = 29; + infbs_cont[CONT_ICFP][icont][usebas] = 30; + infbs_cont[CONT_TAG][icont][usebas] = 2; + exndcf[29][usebas] = 0.37368400; + exndcf[30][usebas] = 1.00000000; + + ret_val = bas_rtdb_do_store(rtdb, bs_name[usebas], bs_tags[1][usebas], + infbs_head[1][usebas], infbs_tags[1][1][usebas], + infbs_cont[1][1][usebas], exndcf[1][usebas], 3, 9, 30); + + printf("inside 321g load\n"); + printf("inside 321g load\n"); + ret_val = bas_print(basis); + printf("inside 321g load\n"); + printf("inside 321g load\n"); + + if (!bas_destroy(basis)) { + printf("error releasing temporary basis handle\n"); + return false; + } + + return true; +} + +bool bas_print(FILE *basisin) { + // routine to print unique basis information that is in core + + int mytags, myucont, myprim, mycoef, basis, len_tag, empty; + int i, j, k, l, ifcont, mygen, mytype, iexptr, icfptr; + char ctype[7][4] = {"S", "P", "D", "F", "G", "H", "I"}; + char cltype[3][4] = {"SP", "SPD"}; + char shell_type[4]; + char blank[17] = " "; + bool ret_val; + + basis = basisin + BASIS_HANDLE_OFFSET; + + ret_val = bas_check_handle(basisin, "bas_print"); + if (!ret_val) return false; + + // print basis set information + printf(" Basis \"%.*s\" -> \"%.*s\"\n", inp_strlen(bs_name[basis]), bs_name[basis], inp_strlen(bs_trans[basis]), bs_trans[basis]); + + mytags = infbs_head[HEAD_NTAGS][basis]; + if (mytags <= 0) { + printf(" Empty basis set \n\n"); + return true; + } + + myucont = infbs_head[HEAD_NCONT][basis]; + myprim = infbs_head[HEAD_NPRIM][basis]; + mycoef = infbs_head[HEAD_NCOEF][basis]; + + /* write(6,2) mytags, myucont, myprim, mycoef + 2 format( + $ ' number of unique tags :',i5/ + $ ' number of unique contractions :',i5/ + $ ' number of unique primitives :',i5/ + $ ' number of unique coefficients :',i5) + */ + + for (i = 1; i <= mytags; i++) { + len_tag = inp_strlen(bs_tags[i][basis]); + empty = (16 - len_tag) / 2; + printf("%.*s%s\n", empty, blank, bs_tags[i][basis]); + + myucont = infbs_tags[TAG_NCONT][i][basis]; +/* write(6,4) myucont,infbs_tags(TAG_NPRIM,i,basis), + $ infbs_tags(TAG_NCOEF,i,basis) + 4 format( + & ' number of contractions:',i5/ + & ' number of primitives :',i5/ + & ' number of coefficients:',i5/) +*/ + ifcont = infbs_tags[TAG_FCONT][i][basis]; + + printf(" Exponent Coefficients \n"); + printf(" ----------- %.*s\n", 60, "----------------"); + + for (j = 1; j <= myucont; j++) { + myprim = infbs_cont[CONT_NPRIM][ifcont][basis]; + mygen = infbs_cont[CONT_NGEN][ifcont][basis]; + + mytype = infbs_cont[CONT_TYPE][ifcont][basis]; + if (mytype < 0) { + strcpy(shell_type, cltype[abs(mytype)]); + } else { + strcpy(shell_type, ctype[mytype]); + } + +/* write(6,5) j, shell_type(1:inp_strlen(shell_type)), +* $ myprim, mygen +* 5 format(/ +* $ ' contraction :', i5/ +* $ ' type : ',a/ +* $ ' number of primitives :', i5/ +* $ ' number of contractions:', i5/) +*/ + iexptr = infbs_cont[CONT_IEXP][ifcont][basis] - 1; + icfptr = infbs_cont[CONT_ICFP][ifcont][basis] - 1; + + for (k = 1; k <= myprim; k++) { + printf(" %2d %2.*s %11.4f", j, 2, shell_type, exndcf[iexptr + k][basis]); + for (l = 1; l <= mygen; l++) { + printf(" %10.6f", exndcf[icfptr + k + (l - 1) * myprim][basis]); + } + printf("\n"); + } + printf("\n"); + + ifcont++; + } + } + +/* If geom is set print out the info about total basis info associated with + the geometry also + + ... not done yet +*/ + + return true; +} + +bool bas_rtdb_load(FILE *rtdb, FILE *geom, FILE *basisin, char *name) { +/* + arguments + rtdb -> valid rtdb handle + geom -> valid geometry handle with info loaded + basisin -> valid basis handle + name -> basis set name that must exist on the rtdb + passed +*/ + int basis; + bool ret_val; + int lentmp; + char tmp[256]; + bool rtdb_status, status; + int i, nat, idum_cont, idum_at; + int j, jstart, jend, jsize; + int kstart, kend, ksize, lsize, icount; + int nbf, iu_cont, myang; + bool foundit; + + rtdb_status = true; + + // check geom and basis handles returns false if either is invalid + + ret_val = geom_check_handle(geom, "bas_rtdb_load"); + if (!ret_val) return false; + ret_val = bas_check_handle(basisin, "bas_rtdb_load"); + if (!ret_val) return false; + + // store geom tag with basis map info + basis = basisin + BASIS_HANDLE_OFFSET; + ibs_geom[basis] = geom; + + // translate "name" to current "context" + bs_name[basis] = name; + len_bs_name[basis] = strlen(name); + if (!context_rtdb_match(rtdb, name, bs_trans[basis])) + bs_trans[basis] = name; + len_bs_trans[basis] = strlen(bs_trans[basis]); + + // generate rtdb names and load information + strcpy(tmp, "basis:"); + strncat(tmp, bs_trans[basis], len_bs_trans[basis]); + lentmp = strlen(tmp) + 1; + + strcpy(tmp + lentmp, ":bs_tags"); + rtdb_status = rtdb_status && rtdb_par_cget(rtdb, tmp, ntags_bsmx, bs_tags[1][basis]); + + strcpy(tmp + lentmp, ":exps and coeffs"); + rtdb_status = rtdb_status && rtdb_par_get(rtdb, tmp, mt_dbl, mxbs_exndcf, exndcf[1][basis]); + + strcpy(tmp + lentmp, ":header"); + rtdb_status = rtdb_status && rtdb_par_get(rtdb, tmp, mt_int, ndbs_head, infbs_head[1][basis]); + + strcpy(tmp + lentmp, ":tags info"); + rtdb_status = rtdb_status && rtdb_par_get(rtdb, tmp, mt_int, ndbs_tags * ntags_bsmx, infbs_tags[1][1][basis]); + + strcpy(tmp + lentmp, ":contraction info"); + rtdb_status = rtdb_status && rtdb_par_get(rtdb, tmp, mt_int, ndbs_ucont * nucont_bsmx, infbs_cont[1][1][basis]); + + // read the basis now get check status of read operations + if (!rtdb_status) { + printf("bas_rtdb_load: ERROR\n"); + printf("basis set is not there\n"); + printf("name requested <|%s|>\n", bs_name[basis]); + printf("translated name requested <|%s|>\n", bs_trans[basis]); + return false; + } + + status = geom_ncent(geom, &nat); + if (nat == 0 || !status) { + printf("bas_rtdb_load: ERROR\n"); + printf("number of centers is zero or weird\n"); + printf("nat = %d\n", nat); + return false; + } +/* + build center to unique center map + + do 00100 i = 1,nat + if (.not.inp_match(infbs_head(HEAD_NTAGS,basis),.true., + & tags(i,geom), + & bs_tags(1,basis),ibs_ce2uce(i,basis))) then + write(6,*)' geom tag was not found in basis tag list rtdb' + write(6,*)' geom tag searched for ',tags(i,geom) + write(6,*)' basis tag list was from basis ',bs_name(basis) + c.... add further diagnostics later + endif + #if defined(BS_DEBUG) + write(6,*)' ibs_ce2uce(',i,') = ',ibs_ce2uce(i,basis) + #endif + 00100 continue +*/ + // build center to unique center map + for (i = 0; i <= nat; i++) { + foundit = false; + for (j = 0; j <= infbs_head[HEAD_NTAGS][basis]; j++) { + if (inp_compare(true, tags[i][geom], bs_tags[j][basis])) { + ibs_ce2uce[i][basis] = j; + foundit = true; + break; + } + } + if (!foundit) { + printf("geom tag was not found in basis tag list rtdb\n"); + printf("geom tag searched for %s\n", tags[i][geom]); + printf("basis tag list was from basis %s\n", bs_name[basis]); + } + } + + // build total # of contractions and center -> contraction range map + idum_cont = infbs_tags[TAG_NCONT][ibs_ce2uce[0][basis]][basis]; + ncont_tot_gb[basis] = idum_cont; + ibs_ce2cnr[0][0][basis] = 1; + ibs_ce2cnr[1][0][basis] = idum_cont; + for (i = 1; i <= nat; i++) { + idum_cont = infbs_tags[TAG_NCONT][ibs_ce2uce[i][basis]][basis]; + ncont_tot_gb[basis] = idum_cont + ncont_tot_gb[basis]; + ibs_ce2cnr[0][i][basis] = ibs_ce2cnr[1][i - 1][basis] + 1; + ibs_ce2cnr[1][i][basis] = ibs_ce2cnr[0][i][basis] + idum_cont - 1; + } + + // build contraction -> center map + for (i = 0; i <= nat; i++) { + jstart = ibs_ce2cnr[0][i][basis]; + jend = ibs_ce2cnr[1][i][basis]; + for (j = jstart; j <= jend; j++) { + ibs_cn2ce[j][basis] = i; + } + } + + // build contraction -> unique contraction map + for (i = 0; i <= nat; i++) { + idum_at = ibs_ce2uce[i][basis]; + jstart = ibs_ce2cnr[0][i][basis]; + jend = ibs_ce2cnr[1][i][basis]; + jsize = jend - jstart + 1; + kstart = infbs_tags[TAG_FCONT][idum_at][basis]; + kend = infbs_tags[TAG_LCONT][idum_at][basis]; + ksize = kend - kstart + 1; + lsize = infbs_tags[TAG_NCONT][idum_at][basis]; + if (jsize == ksize && ksize == lsize) { + icount = 0; + for (j = jstart; j <= jend; j++) { + ibs_cn2ucn[j][basis] = kstart + icount; + icount++; + } + } else { + printf("bas_rtdb_load: ERROR\n"); + printf("contraction range size <-> unique contraction range size mismatch\n"); + printf(" contraction range (%d:%d)\n", jstart, jend); + printf(" unique contraction range (%d:%d)\n", kstart, kend); + printf(" contraction size: %d\n", jsize); + printf(" calculated unique contraction size: %d\n", ksize); + printf(" lookup unique contraction size: %d\n", lsize); + return false; + } + } + + // build nprim_tot_gb, nbf_tot_gb, and + // contraction -> basis function range map + + iu_cont = ibs_cn2ucn[0][basis]; + nbf = infbs_cont[CONT_TYPE][iu_cont][basis]; + nbf = (nbf + 1) * (nbf + 2) / 2; + nbf = nbf * infbs_cont[CONT_NGEN][iu_cont][basis]; + + ibs_cn2bfr[0][0][basis] = 1; + ibs_cn2bfr[1][0][basis] = nbf; + + nbf_tot_gb[basis] = nbf; + nprim_tot_gb[basis] = infbs_cont[CONT_NPRIM][iu_cont][basis]; + for (i = 1; i <= ncont_tot_gb[basis]; i++) { + iu_cont = ibs_cn2ucn[i][basis]; + + nbf = infbs_cont[CONT_TYPE][iu_cont][basis]; + nbf = (nbf + 1) * (nbf + 2) / 2; + nbf = nbf * infbs_cont[CONT_NGEN][iu_cont][basis]; + + ibs_cn2bfr[0][i][basis] = ibs_cn2bfr[1][i - 1][basis] + 1; + ibs_cn2bfr[1][i][basis] = ibs_cn2bfr[0][i][basis] + nbf - 1; + + nbf_tot_gb[basis] += nbf; + nprim_tot_gb[basis] += infbs_cont[CONT_NPRIM][iu_cont][basis]; + } + + // build high angular momentum of this loaded pair + + for (i = 0; i <= ncont_tot_gb[basis]; i++) { + iu_cont = ibs_cn2ucn[i][basis]; + myang = infbs_cont[CONT_TYPE][iu_cont][basis]; + angular_bs[basis] = max(angular_bs[basis], myang); + } + + return ret_val; +} + +bool bas_rtdb_store(FILE *rtdb, char *name, FILE *basisin) { + + /* + Store basis set (not geometry) related info about specified + basis in into the rtdb with the given name + */ + + bool ret_val; + int basis; + + int ret_val = bas_check_handle(basisin, "bas_rtdb_store"); + if (!ret_val) return false; + basis = basisin + BASIS_HANDLE_OFFSET; + ret_val = bas_rtdb_do_store(rtdb, name, + bs_tags[0][basis], infbs_head[0][basis], + infbs_tags[0][0][basis], + infbs_cont[0][0][basis], exndcf[basis], + infbs_head[HEAD_NTAGS][basis], + infbs_head[HEAD_NCONT][basis], + infbs_head[HEAD_NPRIM][basis] + infbs_head[HEAD_NCOEF][basis]); + + return ret_val; +} + +bool bas_rtdb_do_store(FILE *rtdb, char *name, int *tagsin, int *head_array, + int *tags_array, int *ucont_array, double *excfin, + int ntagsin, int nucontin, int nexcf) { +/* + This routine stores the basis set information in the appropriate + data structure on the run-time-data-base (rtdb). + + This is a private routine called by the user level routine + bas_rtdb_store(rtdb, name, basis) + + argument description + C*(*) name -> name of the basis set + C*16(1:ntagsin) tagsin -> name of each tag +*/ + bool status; + char tmp[256]; + int len_name, lentmp; + + bool bas_rtdb_do_store = true; + + status = bas_rtdb_in(rtdb); + + // generate rtdb names and store information + len_name = strlen(name); + strcpy(tmp, "basis:"); + strncat(tmp, name, len_name); + lentmp = strlen(tmp) + 1; + + status = true; + status = status && bas_rtdb_add(rtdb, name); + strncpy(tmp + lentmp, ":bs_tags", 9); + status = status && rtdb_par_cput(rtdb, tmp, ntagsin, tagsin); + + strncpy(tmp + lentmp, ":exps and coeffs", 16); + status = status && rtdb_par_put(rtdb, tmp, mt_dbl, nexcf, excfin); + + strncpy(tmp + lentmp, ":header", 8); + status = status && rtdb_par_put(rtdb, tmp, mt_int, ndbs_head, head_array); + + strncpy(tmp + lentmp, ":tags info", 10); + status = status && rtdb_par_put(rtdb, tmp, mt_int, (ndbs_tags * ntagsin), tags_array); + + strncpy(tmp + lentmp, ":contraction info", 16); + status = status && rtdb_par_put(rtdb, tmp, mt_int, (ndbs_ucont * nucontin), ucont_array); + + // read the basis now and check status of read operations + if (!status) { + printf("bas_rtdb_store: ERROR\n"); + printf("one or more put operations failed\n"); + bas_rtdb_do_store = false; + // add diagnostics later + return bas_rtdb_do_store; + } + + return ret_val; +} + +bool bas_high_angular(FILE *basisin, int *high_angular) { + +// calculate and store high angular momentem function +// for given basis. + + bool ret_val; + int basis, myucont, i; + + ret_val = bas_check_handle(basisin, "bas_high_angular"); + if (!ret_val) { + printf("basis handle not valid\n"); + return false; + } + + basis = basisin + BASIS_HANDLE_OFFSET; + if (angular_bs[basis] > -565) { + *high_angular = angular_bs[basis]; + return true; + } + + myucont = infbs_head[HEAD_NCONT][basis]; + *high_angular = -565; + + for (i = 1; i <= myucont; i++) { + *high_angular = max(*high_angular, infbs_cont[CONT_TYPE][i][basis]); + } + + angular_bs[basis] = high_angular; + return true; +} + +bool gbs_map_clear(FILE *basisin) { + +// routine to clear online map information and basis information + + int basis; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (!bas_check_handle(basisin, "gbs_map_clear")) { + printf("basis handle not valid\n"); + return false; + } + + ifill(ncont_mx, 0, ibs_cn2ucn(1, basis), 1); + ifill(ncont_mx, 0, ibs_cn2ce(1, basis), 1); + ifill(2 * ncont_mx, 0, ibs_cn2bfr(1, 1, basis), 1); + ifill(nat_mx, 0, ibs_ce2uce(1, basis), 1); + ifill(2 * nat_mx, 0, ibs_ce2cnr(1, 1, basis), 1); + ncont_tot_gb[basis] = 0; + nprim_tot_gb[basis] = 0; + nbf_tot_gb[basis] = 0; + + angular_bs[basis] = -565; + + return true; +} + +bool gbs_map_print(FILE *basisin) { + + FILE *mygeom; + int nat, basis, i, myfirst, mylast, mysize, mycenter, myucont; + bool status, ret_val; + + basis = basisin + BASIS_HANDLE_OFFSET; + + // check geom and basis handles returns false if either is invalid + mygeom = ibs_geom(basis); + ret_val = geom_check_handle(mygeom, "gbs_map_print"); + if (!ret_val) return false; + ret_val = bas_check_handle(basisin, "gbs_map_print"); + if (!ret_val) return false; + + // find number of atoms + status = geom_ncent(mygeom, &nat); + + if (nat == 0 || !status) { + printf("gbs_map_print: ERROR\n"); + printf("number of centers is zero or weird\n"); + printf("nat = %d\n", nat); + ret_val = false; + // add diagnostics later + return ret_val; + } + + // print global information + printf("<<< GBS_MAP_PRINT >>>\n"); + printf("total number of atoms : %d\n", nat); + printf("total number of contractions : %d\n", ncont_tot_gb[basis]); + printf("total number of primitives : %d\n", nprim_tot_gb[basis]); + printf("total number of basis functions : %d\n", nbf_tot_gb[basis]); + + // print center based mapping information + printf("\n"); + printf("=============================================================\n"); + printf("center -> unique center map \n"); + printf(" -> contraction range map \n"); + printf("=============================================================\n"); + for (i = 1; i <= nat; i++) { + printf("center: %d maps to unique center: %d\n", i, ibs_ce2uce(i, basis)); + myfirst = ibs_ce2cnr(1, i, basis); + mylast = ibs_ce2cnr(2, i, basis); + mysize = mylast - myfirst + 1; + printf("has %d contractions \n", mysize, myfirst, mylast); + } + + // print contraction based mapping information + printf("\n"); + printf("=============================================================\n"); + printf("contraction -> center map \n"); + printf(" -> unique contraction in basis set \n"); + printf(" -> basis function range \n"); + printf("=============================================================\n"); + + for (i = 1; i <= ncont_tot_gb[basis]; i++) { + mycenter = ibs_cn2ce(i, basis); + myucont = ibs_cn2ucn(i, basis); + myfirst = ibs_cn2bfr(1, i, basis); + mylast = ibs_cn2bfr(2, i, basis); + mysize = mylast - myfirst + 1; + printf("contraction %d is on center: %d\n", i, mycenter); + printf("is represented by unique contraction: %d\n", myucont); + printf("has %d basis functions \n", mysize, myfirst, mylast); + } + + return true; +} + +bool bas_get_exponent(FILE *basisin, int icont, bool unique, double *exp) { + // passed + bool ret_val; + int basis, myucont, icontmax; + int myprim, myexptr; + + ret_val = bas_check_handle(basisin, "bas_get_exponent"); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + if (unique) { + icontmax = infbs_head(HEAD_NCONT, basis); + myucont = icont; + } else { + icontmax = ncont_tot_gb(basis); + myucont = ibs_cn2ucn(icont, basis); + } + ret_val = icont > 0 && icont <= icontmax; + if (!ret_val) { + printf("bas_get_exponent: ERROR\n"); + printf("contraction range for basis is 1:%d\n", icontmax); + printf("information requested for contraction:%d\n", icont); + return false; + } + + myexptr = infbs_cont(CONT_IEXP, myucont, basis); + myprim = infbs_cont(CONT_NPRIM, myucont, basis); + dcopy(myprim, exndcf(myexptr, basis), 1, exp, 1); + /* + for (int i = 0; i < myprim; i++) { + exp[i] = exndcf(myexptr, basis)[i]; + } + */ + + return true; +} + +bool bas_continfo(FILE *basisin, int icont, bool unique, int *nprimo, int *ngeno, int *sphcart) { + + // passed + bool ret_val; + int basis, myucont, icontmax; + + nprimo = -123; + ngeno = -456; + sphcart = -789; + + ret_val = bas_check_handle(basisin, "bas_continfo"); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (unique) { + icontmax = infbs_head(HEAD_NCONT, basis); + } else { + icontmax = ncont_tot_gb(basis); + } + + if (!(icont > 0 && icont <= icontmax)) { + printf("bas_continfo: ERROR\n"); + if (unique) { + printf("unique contraction range for basis is 1:%d\n", icontmax); + } else { + printf("contraction range for basis is 1:%d\n", icontmax); + } + printf("information requested for contraction:%d\n", icont); + return false; + } + + if (unique) { + myucont = icont; + } else { + myucont = ibs_cn2ucn(icont, basis); + } + + // ... no spherical yet 3/94 only cart. + sphcart = 0; + nprimo = infbs_cont(CONT_NPRIM, myucont, basis); + ngeno = infbs_cont(CONT_NGEN, myucont, basis); + + return true; +} + +bool bas_numcont(FILE *basisin, int *numcont, bool unique) { + int basis; + numcont = -6589; + if (!bas_check_handle(basisin, "bas_numcont")) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (unique) { + numcont = infbs_head(HEAD_NCONT, basis); + } else { + numcont = ncont_tot_gb(basis); + } + + return true; +} + +bool bas_numbf(FILE *basisin, int *nbf) { + int basis; + *nbf = -6589; + if (!bas_check_handle(basisin, "bas_numbf")) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + *nbf = nbf_tot_gb(basis); + return true; +} + +bool bas_get_coeff(FILE *basisin, int icont, bool unique, double *coeff) { + bool ret_val; + int basis, myucont, icontmax; + int mycoeffptr, myprim, mygen; + + ret_val = bas_check_handle(basisin, "bas_get_coeff"); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (unique) { + icontmax = infbs_head(HEAD_NCONT, basis); + myucont = icont; + } else { + icontmax = ncont_tot_gb(basis); + myucont = ibs_cn2ucn(icont, basis); + } + + ret_val = (icont > 0) && (icont <= icontmax); + if (!ret_val) { + printf("bas_get_coeff: ERROR\n"); + printf("contraction range for basis is 1:%d\n", icontmax); + printf("information requested for contraction:%d\n", icont); + return false; + } + + mycoeffptr = infbs_cont(CONT_ICFP, myucont, basis); + myprim = infbs_cont(CONT_NPRIM, myucont, basis); + mygen = infbs_cont(CONT_NGEN, myucont, basis); + dcopy((myprim * mygen), exndcf(mycoeffptr, basis), 1, coeff, 1); + + return true; +} + +bool bas_set_exponent(FILE *basisin, int icont, bool unique, double *exp, int nexp) { + bool ret_val; + int basis, myucont, icontmax; + int myexptr, myprim; + + ret_val = bas_check_handle(basisin, "bas_set_exponent"); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (unique) { + icontmax = infbs_head(HEAD_NCONT, basis); + myucont = icont; + } else { + icontmax = ncont_tot_gb(basis); + myucont = ibs_cn2ucn(icont, basis); + } + + ret_val = (icont > 0) && (icont <= icontmax); + if (!ret_val) { + printf("bas_set_exponent: ERROR\n"); + printf("contraction range for basis is 1:%d\n", icontmax); + printf("information requested for contraction:%d\n", icont); + return false; + } + + myexptr = infbs_cont(CONT_IEXP, myucont, basis); + myprim = infbs_cont(CONT_NPRIM, myucont, basis); + ret_val = (myprim == nexp); + if (!ret_val) { + printf("bas_set_exponent: ERROR\n"); + printf("input and stored number of exponents (nprim) differ\n"); + printf("input nprim: %d\n", nexp); + printf("stored nprim: %d\n", myprim); + return false; + } + + dcopy(nexp, exp, 1, exndcf(myexptr, basis), 1); + + return true; +} + +bool bas_set_coeff(FILE *basisin, int icont, bool unique, double *coeff, int ncoeff) { + bool ret_val; + int basis, myucont, icontmax; + int mycoeffptr, myprim, mygen; + + ret_val = bas_check_handle(basisin, "bas_set_coeff"); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + + if (unique) { + icontmax = infbs_head(HEAD_NCONT, basis); + myucont = icont; + } else { + icontmax = ncont_tot_gb(basis); + myucont = ibs_cn2ucn(icont, basis); + } + + ret_val = (icont > 0) && (icont <= icontmax); + if (!ret_val) { + printf("bas_set_coeff: ERROR\n"); + printf("contraction range for basis is 1:%d\n", icontmax); + printf("information requested for contraction:%d\n", icont); + return false; + } + + mycoeffptr = infbs_cont(CONT_ICFP, myucont, basis); + myprim = infbs_cont(CONT_NPRIM, myucont, basis); + mygen = infbs_cont(CONT_NGEN, myucont, basis); + + ret_val = (ncoeff == (myprim * mygen)); + if (!ret_val) { + printf("bas_set_coeff: ERROR\n"); + printf("input and stored number of coefficients (nprim*ngen) differ\n"); + printf("input nprim*ngen: %d\n", ncoeff); + printf("stored nprim*ngen: %d\n", (myprim * mygen)); + return false; + } + + dcopy(ncoeff, coeff, 1, exndcf(mycoeffptr, basis), 1); + + return true; +} + +bool bas_rtdb_out(FILE *rtdb) { + bool ret_val; + + ret_val = rtdb_par_put(rtdb, "basis:nbasis", MT_INT, 1, nbasis_rtdb) && + rtdb_par_cput(rtdb, "basis:names", nbasis_rtdb, bs_names_rtdb); + if (!ret_val) { + printf(" bas_rtdb_out: rtdb is corrupt "); + } + + return bas_rtdb_out; +} + +bool bas_rtdb_add(FILE *rtdb, char *name) { + int basis; + bool ret_val, status; + int ln; + + // See if name is on the rtdb already + ln = strlen(name); + status = bas_rtdb_in(rtdb); + ret_val = true; + + for (basis = 1; basis <= nbasis_rtdb; basis++) { + if (strncmp(name, bs_names_rtdb[basis], ln) == 0) { + return ret_val; + } + } + + // Name is not present ... add and rewrite info + if (nbasis_rtdb == nbasis_rtdb_mx) { + printf("bas_rtdb_add: too many basetries on rtdb %s\n", name); + return false; + } + + nbasis_rtdb++; + strcpy(bs_names_rtdb[nbasis_rtdb], name); + len_bs_rtdb[nbasis_rtdb] = ln; + + ret_val = bas_rtdb_out(rtdb); + if (!ret_val) { + printf("bas_rtdb_add: rtdb error adding %.*s\n", ln, name); + return ret_val; + } + + return true; +} + +bool bas_print_all() { + bool ret_val; + int basis, basin; + + ret_val = true; + for (basis = 1; basis <= nbasis_bsmx; basis++) { + if (bsactive(basis)) { + basin = basis - BASIS_HANDLE_OFFSET; + ret_val = ret_val && bas_print(basin); + } + } + + return ret_val; +} + +void bas_err_info(char *info) { + int bas, basin; + int nbas; + bool status; + + /* + For internal use of the basis set routines only: print out + info of known basis sets to aid in diagnosing a problem + */ + nbas = 0; + for (bas = 1; bas <= nbasis_bsmx; bas++) { + if (bsactive(bas)) { + nbas++; + } + } + printf("%s: open basis sets: %d\n", info, nbas); + + nbas = 0; + for (bas = 1; bas <= nbasis_bsmx; bas++) { + if (bsactive(bas)) { + basin = bas - BASIS_HANDLE_OFFSET; + status = bas_print(basin); + } + } + + if (nbasis_rtdb > 0) { + printf("%s: basis sets in current rtdb %d\n", info, nbasis_rtdb); + for (bas = 1; bas <= nbasis_rtdb; bas++) { + printf("number: %d basis set name: %.*s\n", bas, len_bs_rtdb[bas], bs_names_rtdb[bas]); + } + } +} + +bool bas_rtdb_in(FILE *rtdb) { + bool ret_val; + int bas; + /* + load in info about known basis sets ... this is more + for diagnostic and debugging purposes + */ + ret_val = false; + nbasis_rtdb = 0; + if (rtdb_par_get(rtdb, "basis:nbasis", MT_INT, 1, &nbasis_rtdb)) { + if (!rtdb_par_cget(rtdb, "basis:names", nbasis_rtdb_mx, bs_names_rtdb)) { + printf("bas_rtdb_in: rtdb corrupt\n"); + } else { + for (bas = 1; bas <= nbasis_rtdb; bas++) { + len_bs_rtdb[bas] = inp_strlen(bs_names_rtdb[bas]); + } + ret_val = true; + } + } + + return ret_val; +} + +bool bas_cn2ce(FILE *basisin, int cont, int *center) { + bool ret_val; + int basis; + + ret_val = bas_check_handle(basisin); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + ret_val = cont > 0 && cont <= ncont_tot_gb(basis); + if (!ret_val) { + printf("bas_cn2ce: invalid contraction information\n"); + printf("contraction range is 1:%d\n", ncont_tot_gb(basis)); + printf("input contraction was: %d\n", cont); + return false; + } + center = ibs_cn2ce(cont, basis); + + return true; +} + +bool bas_cn2bf(FILE *basisin, int cont, int *ifirst, int *ilast) { + bool ret_val; + int basis; + + ret_val = bas_check_handle(basisin); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + ret_val = cont > 0 && cont <= ncont_tot_gb(basis); + if (!ret_val) { + printf("bas_cn2bf: invalid contraction information\n"); + printf("contraction range is 1:%d\n", ncont_tot_gb(basis)); + printf("input contraction was: %d\n", cont); + return false; + } + + ifirst = ibs_cn2bfr(1, cont, basis); + ilast = ibs_cn2bfr(2, cont, basis); + + return true; +} + +bool bas_ce2cnr(FILE *basisin, int center, int ifirst, int ilast) { + bool ret_val; + int basis, nat; + + ret_val = bas_check_handle(basisin); + if (!ret_val) return false; + + basis = basisin + BASIS_HANDLE_OFFSET; + ret_val = geom_ncent(ibs_geom(basis), nat); + if (nat == 0 || !ret_val) { + printf("bas_ce2cnr: ERROR\n"); + printf("number of centers is zero or weird\n"); + printf("nat = %d\n", nat); + // add diagnostics later + return false; + } + + ret_val = center > 0 && center <= nat; + if (!ret_val) { + printf("bas_ce2cnr: invalid center information\n"); + printf("contraction range is 1:%d\n", nat); + printf("input contraction was: %d\n", center); + return false; + } + + return true; +} + +bool bas_add_ucnt(FILE *basis, char *tag, int l_value, int ngen, int nprim, + double *expnt, double *coeffs, int ldc) { + bool ret_val; + int ind; // Index into basis function structures + int free; // Free space pointer + int i, itag, jtag, iu_cont, ntags; // Locals + + /* + adds a new general contraction on the specified tag. If the + tag is not present it will also add that by calling bas_add_utag + */ + + ret_val = bas_check_handle(basis, "bas_add_ucnt"); + if (!ret_val) return false; + ind = basis + BASIS_HANDLE_OFFSET; + + // Make sure that the tag is in the list + ret_val = bas_add_utag(basis, tag, &itag); + if (!ret_val) return false; + + // Update header information about all unique contractions on all tags + free = infbs_head[HEAD_NPRIM][ind] + infbs_head[HEAD_NCOEF][ind] + 1; + if ((free+nprim*ngen+nprim-1) > mxbs_exndcf) { + printf("bas_add_ucnt: too many prims/coeffs\n"); + return false; + } + if (infbs_head[HEAD_NCONT][ind]+1 > nucont_bsmx) { + printf("bas_add_ucnt: too many contractions\n"); + return false; + } + + infbs_head[HEAD_NCONT][ind] = infbs_head[HEAD_NCONT][ind] + 1; + infbs_head[HEAD_NPRIM][ind] = infbs_head[HEAD_NPRIM][ind] + nprim; + infbs_head[HEAD_NCOEF][ind] = infbs_head[HEAD_NCOEF][ind] + ngen*nprim; + + ntags = infbs_head[HEAD_NTAGS][ind]; + if (itag != ntags) { + for (jtag = ntags; jtag >= itag+1; jtag--) { + // Shuffle data+pointers for following tags up one contraction + for (iu_cont = infbs_tags[TAG_LCONT][jtag][ind]; + iu_cont >= infbs_tags[TAG_FCONT][jtag][ind]; iu_cont--) { + for (i = 1; i <= ndbs_ucont; i++) { + infbs_cont[i][iu_cont+1][ind] = infbs_cont[i][iu_cont][ind]; + } + } + // Increment first and last contractions on following tags + infbs_tags[TAG_FCONT][jtag][ind] = infbs_tags[TAG_FCONT][jtag][ind] + 1; + infbs_tags[TAG_LCONT][jtag][ind] = infbs_tags[TAG_LCONT][jtag][ind] + 1; + } + } + + // Increment basis info on this tag + infbs_tags[TAG_NCONT][itag][ind] = infbs_tags[TAG_NCONT][itag][ind] + 1; + infbs_tags[TAG_NPRIM][itag][ind] = infbs_tags[TAG_NPRIM][itag][ind] + nprim; + infbs_tags[TAG_NCOEF][itag][ind] = infbs_tags[TAG_NCOEF][itag][ind] + nprim*ngen; + if (infbs_tags[TAG_FCONT][itag][ind] == 0) { + if (itag != ntags) { + printf("bas_add_ucnt: tag error %d\n", itag); + } + infbs_tags[TAG_FCONT][itag][ind] = infbs_head[HEAD_NCONT][ind]; + infbs_tags[TAG_LCONT][itag][ind] = infbs_head[HEAD_NCONT][ind]; + } else { + infbs_tags[TAG_LCONT][itag][ind] = infbs_tags[TAG_LCONT][itag][ind] + 1; + } + + iu_cont = infbs_tags[TAG_LCONT][itag][ind]; // Index of new contraction + + infbs_cont[CONT_TYPE][iu_cont][ind] = l_value; + infbs_cont[CONT_NPRIM][iu_cont][ind] = nprim; + infbs_cont[CONT_NGEN][iu_cont][ind] = ngen; + infbs_cont[CONT_TYPE][iu_cont][ind] = l_value; + infbs_cont[CONT_IEXP][iu_cont][ind] = free; + infbs_cont[CONT_ICFP][iu_cont][ind] = free + nprim; + + // Copy real data over + memcpy(&exndcf[free][ind], expnt, nprim * sizeof(double)); + free = free + nprim; + for (i = 1; i <= ngen; i++) { + memcpy(&exndcf[free][ind], &coeffs[(i-1)*ldc], nprim * sizeof(double)); + free = free + nprim; + } + /* + write(6,*) ' expnt input ', nprim + call output(expnt, 1, nprim, 1, 1, nprim, 1, 1) + write(6,*) ' coeffs input ', nprim, ngen, ldc + call output(coeffs, 1, nprim, 1, ngen, ldc, ngen, 1) + + Done + */ + + return true; +} + +bool bas_add_utag(FILE *basisin, char *tag, int *itag) { + bool ret_val; + int basis; // [local] index into basis arrays + + // Add the unique tag to the list of tags in the basis, + // incrementing the no. of tags if necessary. + // Return in itag the index of the unique tag + + ret_val = bas_check_handle(basisin, "bas_add_utag"); + if (!ret_val) return false; + basis = basisin + BASIS_HANDLE_OFFSET; + + for (*itag = 1; *itag <= infbs_head[HEAD_NTAGS][basis]; (*itag)++) { + if (inp_compare(true, bs_tags[*itag][basis], tag)) return true; + } + + // No match found ... append new tag to the list + + *itag = infbs_head[HEAD_NTAGS][basis] + 1; + if (*itag > ntags_bsmx) { + printf("bas_add_utag: too many tags %d\n", itag); + return false; + } + + infbs_head[HEAD_NTAGS][basis] = itag; + bs_tags[itag][basis] = tag; + + return true; +} diff --git a/src/basis/doc/api b/src/basis/doc/api new file mode 100644 index 0000000..a6d6b59 --- /dev/null +++ b/src/basis/doc/api @@ -0,0 +1,138 @@ + + + + Program main + + ---------------------- + + fix rtdb for arrays of characters + + + ---------------------- + + context management + + + ---------------------- + + get/set coords,charges,tags,masses,zmat(?),ncenters, + + map 'geometry' -> name of geometry + + logical geom_load(rtdb, 'geometry', geom) + logical geom_store(rtdb, 'geometry', geom) + + ncent = geom_ncenter(geom) + call geom_tag(geom, icent, tag) + call geom_cent_coords(geom, icent, coords) + call geom_cent_charge(geom, icent, charge) + ... + call geom_cent_info(geom, icent, tag, coords, charge, mass, ...) + + logical geom_zmat_defined() + + nvariables = geom_zmat_nvars(geom) + nconstants .... + + call geom_cart_get(geom, all info) + call geom_cart_set(geom, all info) + + call geom_zmat_get + call geom_zmat_set + + print + + + Also on the DB + + - list of known geometry names + + + ---------------------- + + map 'mo basis' -> name of basis descriptor + + ---------------------- + + logical basis_load(name_of_basis_descriptor, geom, basis) + nbasis_func = basis_nfunc(basis) + nbasis_shell = basis_nshell(basis) + natoms / basis_centers = + map atom/center<->shell<->bf + get/set exponents/contraction coeffs + shell info (angular, gcontract, spherical/cart) + highest ang. mom. + print + load/store + + On the data-base is + + - list of known basis set names + - + + ---------------------- + + Cannot tweak geometry or basis between init/term calls + +... control + int_initialize(geom, num_basis, basis_array) : generate internal int structures +................................................................................. +# not needed if batmol writes to rtdb properly + int_initialize_tape10 () : generate internal int structures (batmol?) +................................................................................. + int_terminate() : throw away internal int structures + int_print_known_basis() + int_set_eri_timing() + int_report_eri_timings() + int_mem(max1e, maxg, mscratch_1e, mscratch_2e) + int_mem_one(max1e, mscratch_1e) + int_mem_4(maxg, mscratch_2e) + int_mem_3(max3, mscratch_3_2e) + int_mem_2(max2, mscratch_2_2e) + int_mem_3ov(max3ov, mscratch_3ov) + +... two electron +. 4 center 2e integrals + eri = + int_two_4(bra_basis, ket_basis, ish, jsh, ksh, lsh, lscr, + scr, eri) + lab_two_4(bra_basis, ket_basis, ish, jsh, ksh, lsh, zerotol, + canonicalize, eri, nints, ilab, jlab, klab, llab) + +. 3 center 2e integrals + eri = + int_two_3 (bra_basis, ket_basis, ish, jsh, ksh, lscr, scr, eri) + lab_two_3 (bra_basis, ket_basis, canonical_bra, canonical_both, ish, jsh, ksh, zerotol, + eri, nints, ilab, jlab, klab) + +. 2 center 2e integrals + eri = + int_two_2 (bra_basis, ket_basis, ish, jsh, lscr, scr, eri) + lab_two_2 (bra_basis, ket_basis, canonical_both, ish, jsh, zerotol, lscr, scr, eri, + nints, ilab, jlab) + +... one electron integrals + int_one_ke_basic (i_basis, j_basis, ish, jsh, lscr, scr, T) + int_one_pe_basic (i_basis, j_basis, ish, jsh, lscr, scr, V) + int_one_ov_basic (i_basis, j_basis, ish, jsh, lscr, scr, S) + int_one_h1_basic (i_basis, j_basis, ish, jsh, lscr, scr, H1) + int_one_all_basic(i_basis, j_basis, ish, jsh, lscr, scr, S, T, V) + lab_one_ke (i_basis, j_basis, ish, jsh, zerotol, ilab, jlab, T, numt) + lab_one_pe (i_basis, j_basis, ish, jsh, zerotol, ilab, jlab, V, numv) + lab_one_ov (i_basis, j_basis, ish, jsh, zerotol, ilab, jlab, S, nums) + lab_one_h1 (i_basis, j_basis, ish, jsh, zerotol, ilab, jlab, H1, numh1) + lab_one_all(i_basis, j_basis, ish, jsh, zerotol, ilab, jlab, S, T, V, numstv) + + one_3c_int = + int_one_3ov(i_basis, j_basis, k_basis, ish, jsh, ksh, lscr, + scr, OV3) + lab_one_3ov(i_basis, j_basis, k_basis, ish, jsh, ksh, zerotol, + OV3, ilab, jlab, klab, numov3) + + + int_mpole(i_basis, j_basis, Lvalue, ish, jsh, lscr, scr, MPINTS) + lab_mpole(i_basis, j_basis, Lvalue, ish, jsh, MPINTS, ilab, jlab, zerotol) + + + periodic versions (with k vector) + ---------------------- + \ No newline at end of file diff --git a/src/basis/doc/basis.doc b/src/basis/doc/basis.doc new file mode 100644 index 0000000..e9fef9f --- /dev/null +++ b/src/basis/doc/basis.doc @@ -0,0 +1,149 @@ +/* The basis set objects are written in C. + +Proposal for basis set objects (rjh/rak) + + + 1) Currently have only general and segmented contractions of + primitive gaussians but other basis sets should be anticipated + + 2) The whole GTO basis is either cartesian or spherical harmonic + + 3) Basis functions are associated with atomic tags, not coordinates, + the tags providing the connection to a geometry + + 4) All basis functions associated with an 'atomic' center will be + numbered consecutively + +5) General Basis Set Class: + +**** Attributes: +Basis_type: Contracted Gaussian + or pseudo-potentails + or plane wave + or .?.?.?.?. + +if (Basis_type.eq.1) (sub class definition) + number_of_tags: number of tags with information to be given/retrieved. + (NOTE: generally equal to the number of centers to be + defined by the geometry object.) + cartesian: is it cartesian or spherical (transformed). + nprim_tot:: total number of primitive gaussians. + ncoeff_tot:: total number of contractraction coeffs + nshell_tot:: total number of shells (in the normal sense). + nbf_tot:: total number of basis functions (in the normal sense). + + + + for each (tag (1 .. number_of_tags) (a.k.a. center)) + tag: name of atomic center (o, bond_function, ghost center) + contraction_type: Segmented or General? + (note: basis sets may have mixed segmented and + general contracted centers) + ngen: =1 (segmented) >1 (general). + nshell: number of shells for this tag (in normal sense). + :nGshell: number of generally contracted shells. + (what is the limit?? tradeoff memory vs cpu) + nbf_on_tag: number of basis functions for this tag. + :nbf_cart: number of cartesian basis functions + (note: evaluation most likely always in cartesians) + :nbf_sph: number of spherical basis functions. + nprim: number of primitives in contraction. + + for each (contraction set) [general or segmented] + type basis function type = GTO (redundant??) + L angular momentum s,p,d = 0, 1, 2 + Ltype =0 use only angular momentum L + =1 implies use of all angular momenta up to L + e.g., sp shells (like gaussian) or + spd shells (Rydberg, bond functions) + num_cnt number of contractions coefs (always=1 for segmented) + nbf number of basis functions in contraction (external view) + :nbf_cart: number of cartesian basis functions in contraction + :nbf_sph: number of spherical basis functions in contraction + nprim number of primitives in contraction set + coef(nprim,num_cnt) contraction coefs + ex(nprim) exponents + + +proposal: (some of what we need to decide!!) +. above atributes that are :attribute: are to be used only by the api + and integral routines. +. attributes that are atribute:: are derived some how. + + +other pointer arrays etc can be defined/derived from this information +and the goemetry object and thus are application dependent. There is +no requirement that these pointer arrays match across applications/ +modules/libraries. Mappings to the final integral code could be +supplied by the api. The major hash will be to determine what is +defined a priori and what is derived information. e.g., the total +number of basis functions for a basis: is fixed but for a +molecular or periodic system it is unknown until the geometry object +defines the scope. + +else + it ain't been defined yet. +endif + +**** Operations: (lean and mean) +query_on: scope_set, number_of_tags, cartesian, nprim_tot, ncoeff_tot, nbf_tot etc. +open: +close: +define: (later not now). +set_scope: + + + 6) For compact and portable representation in the database this is + compacted into five entries. + + a) dimension information + + b) character information + + c) pointer information + + d) integer information + + e) real information + + 7) All basis set info is named as if components of a basis module + so all names are of the form + + basis:: ... + + 8) A data base entry basis:list contains a list of the names + of all basis sets in the database so that it is easy to + examine what is in the database + + 9) a mixed basis set can be a sum of two basis sets object subclasses?? + e.g., planewave + contracted gaussian + pseudo-potential + contracted gaussian. + + + +objects: + basis set --> name --> on rtdb +operations: + ---------------------- + + map 'mo basis' -> name of basis descriptor + + ---------------------- + + logical basis_load(name_of_basis_descriptor, geom, basis) + nbasis_func = basis_nfunc(basis) + nbasis_shell = basis_nshell(basis) + natoms / basis_centers = + map atom/center<->shell<->bf + get/set exponents/contraction coeffs + shell info (angular, gcontract, spherical/cart) + highest ang. mom. + print + load/store + + On the data-base is + + - list of known basis set names + - + +*/ \ No newline at end of file diff --git a/src/basis/doc/basis.output b/src/basis/doc/basis.output new file mode 100755 index 0000000..9c9b9ac --- /dev/null +++ b/src/basis/doc/basis.output @@ -0,0 +1,139 @@ + SI 0 + S 20 1.00 + 3948000.00000000 0.00000204 + 591100.00000000 0.00001584 + 134500.00000000 0.00008336 + 38120.00000000 0.00035136 + 12460.00000000 0.00127660 + 4504.00000000 0.00415191 + 1758.00000000 0.01230300 + 729.10000000 0.03331020 + 318.00000000 0.08098450 + 144.60000000 0.17029000 + 67.97000000 0.28687900 + 32.82000000 0.33034000 + 16.03000000 0.19660200 + 7.39600000 0.03545350 + 3.66100000 -0.00053520 + 1.82300000 0.00161465 + 0.91470000 -0.00037274 + 0.33930000 0.00014623 + 0.15000000 -0.00007894 + 0.06438000 0.00001928 + S 20 1.00 + 3948000.00000000 -0.00000054 + 591100.00000000 -0.00000422 + 134500.00000000 -0.00002218 + 38120.00000000 -0.00009360 + 12460.00000000 -0.00034012 + 4504.00000000 -0.00111061 + 1758.00000000 -0.00330878 + 729.10000000 -0.00911602 + 318.00000000 -0.02287900 + 144.60000000 -0.05171190 + 67.97000000 -0.09990910 + 32.82000000 -0.15274700 + 16.03000000 -0.12750800 + 7.39600000 0.09469630 + 3.66100000 0.41403600 + 1.82300000 0.46793400 + 0.91470000 0.17392700 + 0.33930000 0.00843895 + 0.15000000 -0.00099807 + 0.06438000 0.00036210 + S 20 1.00 + 3948000.00000000 0.00000014 + 591100.00000000 0.00000108 + 134500.00000000 0.00000569 + 38120.00000000 0.00002395 + 12460.00000000 0.00008724 + 4504.00000000 0.00028416 + 1758.00000000 0.00084984 + 729.10000000 0.00233527 + 318.00000000 0.00590466 + 144.60000000 0.01334610 + 67.97000000 0.02628890 + 32.82000000 0.04074260 + 16.03000000 0.03614760 + 7.39600000 -0.03039230 + 3.66100000 -0.13596100 + 1.82300000 -0.25014400 + 0.91470000 -0.15805000 + 0.33930000 0.36965500 + 0.15000000 0.61771800 + 0.06438000 0.22251400 + S 1 1.00 + 0.91470000 1.00000000 + S 1 1.00 + 0.33930000 1.00000000 + S 1 1.00 + 0.15000000 1.00000000 + S 1 1.00 + 0.06438000 1.00000000 + P 12 1.00 + 1780.00000000 0.00020121 + 421.80000000 0.00174937 + 136.70000000 0.00948141 + 51.81000000 0.03723130 + 21.60000000 0.11076300 + 9.56300000 0.23793300 + 4.35000000 0.35369100 + 2.00600000 0.32883900 + 0.92050000 0.13237300 + 0.35000000 0.01033000 + 0.13810000 -0.00015031 + 0.05338000 0.00026581 + P 12 1.00 + 1780.00000000 -0.00004272 + 421.80000000 -0.00037704 + 136.70000000 -0.00202240 + 51.81000000 -0.00812833 + 21.60000000 -0.02422720 + 9.56300000 -0.05438250 + 4.35000000 -0.07990510 + 2.00600000 -0.08889580 + 0.92050000 0.01839970 + 0.35000000 0.33509600 + 0.13810000 0.53228800 + 0.05338000 0.25437400 + P 1 1.00 + 0.92050000 1.00000000 + P 1 1.00 + 0.35000000 1.00000000 + P 1 1.00 + 0.13810000 1.00000000 + P 1 1.00 + 0.05338000 1.00000000 + D 1 1.00 + 0.12600000 1.00000000 + D 1 1.00 + 0.32100000 1.00000000 + D 1 1.00 + 0.81700000 1.00000000 + D 1 1.00 + 2.08200000 1.00000000 + F 1 1.00 + 0.16900000 1.00000000 + F 1 1.00 + 0.34100000 1.00000000 + F 1 1.00 + 0.68800000 1.00000000 + G 1 1.00 + 0.32000000 1.00000000 + G 1 1.00 + 0.70500000 1.00000000 + H 1 1.00 + 0.58300000 1.00000000 + S 1 1.00 + 0.02600000 1.00000000 + P 1 1.00 + 0.01920000 1.00000000 + D 1 1.00 + 0.04680000 1.00000000 + F 1 1.00 + 0.07350000 1.00000000 + G 1 1.00 + 0.15100000 1.00000000 + H 1 1.00 + 0.32300000 1.00000000 + **** \ No newline at end of file diff --git a/src/basis/doc/robert.doc b/src/basis/doc/robert.doc new file mode 100644 index 0000000..783d62e --- /dev/null +++ b/src/basis/doc/robert.doc @@ -0,0 +1,218 @@ + + +1) Minimize implementation effort + +2) Simplify data structures so that are flattened + more readily + +3) Enable local integral routines to work directly + from API interface and/or internal data structures + +4) Store info in the database to avoid having a + zillion small files floating around + + +In the database we store just the basis set description +(i.e., the atomic basis sets for the unique atom tags) +in as simple a format as possible + +In core, we have in addition mapping arrays that build +the basis set from the geometry and the basis set description + + +How to store the atomic basis set compactly, but so that +it is readily stored and efficiently used? + + The integral routines will be given basis set handles and + shell indices. These will be used to lookup + the shell info (l-value, ngen, nprim) and find pointers + to the contraction info. Since Fortran cannot have pointers + returned to it from a C interface we have to either store + the stuff both on the C and Fortran sides, or do it + all in Fortran (I know, double ugh). I see no point + in doing things twice. + + Since we are stuck with F77 we have no structures and + are back using simple offsets etc. This actually makes + storing the info externally easier since the internal + representation is flat. + + +Detailed data structures ... derive from their usage by your +integral routines. + + int_2e_4c(ibasis, jbasis, ish, jsh, ksh, lsh, ...) + + check basis handles + + get info (type, nprim, ngen, coords) on each shell + + find pointers to coeffs/exponents for each shell + (this implies that they are stored packed into a + single array and we have offsets stored) + + branch to the fastest routine depending on if generally contracted, + the angular momentum, if it is an sp shell, ... + + in your API + + call the primitive evaluation routine with explicit + coord/coeff/exponents + + + So it seems that we have very similar data structures to the + present int.h, except that the basis info is only stored for + unique atom types + + Now do the mapping in detail + + + if (ibasis .le.0 .or. ibasis .gt. nbasis) call errquit(...) + + if (ish .le. 0 .or. ish .gt. nshell(ibasis)) call errquit(...) + + iuniq = shell_uniq(ish, ibasis) ... map shell to no. of the shell info + for unique tags only + + itype = shell_type(iuniq, ibasis) (1, 2, 3 for s, p, d + -1, -2, ... for sp, spd, ... shells) + + iprim = shell_nprim(iuniq, ibasis) + + igen = shell_nprim(iuniq, ibasis) + + iexpnt= shell_expt(iuniq, ibasis) ... offset in exp(1, ibasis) where + this shells exponents start + + icoeff= shell_cofpt(iuniq, ibasis) ... offset in coeff(1, ibasis) .... + + + icent= shell_cent(ish, ibasis) ... center no. for this shell to get coords + (for efficiency should grab the + coords from the geometry) + + + Should be rolling at this point. + + Also need the following arrays to support the other basis set + routines + + cent_to_sh(1:2, icent, ibasis) (contains hi-lo) + cent_to_bf(1:2, icent, ibasis) + sh_to_bf(1:2, ish, ibasis) + + + The info about each shell is simply + + integer type, nprim, ngen + real coeff(nprim,ngen), expnt(nprim) + + + Thus, the atomic basis set is just + + integer nshell, nprim_tag, ncoeff_tag + integer type(nshell), nprim(nshell), ngen(nshell), + cofpt(nshell), expt(nsehll) + real coeff(ncoeff_tag), expnt(nprim_tag) + + + For external storage this can be compactly represented as + ... and there is no reason why the data cannot be also used + this way (so that coefpt and expt provide offsets into rdata) + + integer dim_info(3) + integer idata(5*nshell) + real rdata(ncoeff_tag+nprim_tag) + + (the rtdb can automatically allocate the MA arrays and read into them) + + These could be stored on the rtdb as + + basis:basis_name:tag:dim_info + basis:basis_name:tag:idata + basis:basis_name:tag:rdata + + along with a summary of all unique tag info + + integer nshell_total, nprim_total, idata_total, rdata_total + + basis:basis_name:dim_info -> integer dim_info(4) + + + + However, we can make things even easier by storing the whole + damn lot in one data structure since it will always be possible + to store info on the unqiue atom centers (even if the whole + periodic table is in there!). Thus, my recomendation is that + the data base contain the following + + basis:basis_name:dim_info integer + basis:basis_name:tags character + basis:basis_name:tdata integer + basis:basis_name:idata integer + basis:basis_name:rdata double precision + + Where + + dim_info(1) -> nshell_uniq_total = total no. of shells on the unique tags + dim_info(2) -> nprim_uniq_total = total no. of prims on the unique tags + dim_info(3) -> idata_uniq_total = total length of idata + dim_info(4) -> idata_uniq_total = total length of rdata + dim_info(5) -> ntags_uniq = no. of unique tags + + tags(1:ntags_uniq) = character array of tags (cannot be allocated + using MA !!) + + tdata(1, itag_uniq) = first unique shell on this tag + tdata(2, itag_uniq) = last last shell on this tag + + idata(1, ish_uniq) = type of shell + idata(2, ish_uniq) = nprim in shell + idata(3, ish_uniq) = ngen of shell + idata(4, ish_uniq) = offset into rdata for coeffs + idata(5, ish_uniq) = offset into rdata for exponents + idata(6, ish_uniq) = no. of bf in this shell + + + + To load this lot into core and build the data structures + on the fly : + + logical function basis_load(rtdb, name, igeom, ibasis) + + 0) look for translations of name within the current or higher + context using context_rtdb_match(). With the name or available + translation look for basis:basis_name:dim_info ... if this is there + then the basis set is defined. Can adopt a default at this + point if desired. Check that have statically allocated enuf + space to read in the unique tags. + + rtdb_cget( tags ) + rtdb_ma_get (tdata, rdata, idata) + + 1) Get tags/coords info from the geometry (note .. only one geometry + being used by the integrals at a time ... I would suggest that + the geometry handle be removed from the int_init() call and + be stored internal to each basis sets structure ... this then + gives us a mechanism to compute integrals between different + geometries (this sounds worth thinking about more)). + + 2) Loop thru centers checking that have a basis defined for that + tag and accumulate the no. of shells and basis functions. + At same time build map from atoms to shells and bf and + map from shells to unique shell no. + + +Done. + +How this info gets onto the database is another problem. I would +suggest that the input program provides the info in nearly this form +to a basis set routine for output to the database. Since the input +routines want to be very general it's best to let them worry about +the details and live with a very simple basis set interface. We also +need to consider how to handle plane waves, giaos etc ... let's talk +about this and also to Jeff about giaos before casting this in +FORTRAN. I think that the above will suffice for the GTO basis +sets and we can add additional RTDB entries for the plane waves etc. + +Robert \ No newline at end of file diff --git a/src/basis/geobasmapP.h b/src/basis/geobasmapP.h new file mode 100644 index 0000000..b6c5b97 --- /dev/null +++ b/src/basis/geobasmapP.h @@ -0,0 +1,29 @@ +#ifndef _GEOBASMAPP_H +#define _GEOBASMAPP_H +/* + NOTE: this MUST follow basP.fh in the include order + + these are all in core + mapping arrays atoms <-> contr <-> bfn (maybe add shells later) + + contraction -> unique_contr :: ibs_cn2ucn(ncont,nbasis) + contraction -> center_number :: ibs_cn2ce (ncont,nbasis) + center -> unique_center :: ibs_ce2uce(nat,nbasis) + contraction -> basis function range :: ibs_cn2bfr(2,ncont,nbasis) + centers -> contraction range :: ibs_ce2cnr(2,nat,nbasis) +*/ +#ifdef __cplusplus +extern "C" { +#endif + int ibs_cn2ucn(int ncont, int nbasis); + int ibs_cn2ce(int ncont, int nbasis); + int ibs_ce2uce(int nat, int nbasis); + int ibs_cn2bfr(int ncont, int nbasis); + int ibs_ce2cnr(int nat, int nbasis); + + int ncont_tot_gb, nprim_tot_gb, nbf_tot_gb, ibs_geom; +#ifdef __cplusplus +} +#endif + +#endif // _GEOBASMAPP_H diff --git a/src/basis/newbasis.c b/src/basis/newbasis.c new file mode 100644 index 0000000..96869f5 --- /dev/null +++ b/src/basis/newbasis.c @@ -0,0 +1,11 @@ +#include + +void bas_dummmmmm() { + int i; + i = 0; +} + +int bas_print_known(FILE *rtdb) { + return 0; +} + diff --git a/src/basis/testbasis.c b/src/basis/testbasis.c new file mode 100644 index 0000000..d9190ab --- /dev/null +++ b/src/basis/testbasis.c @@ -0,0 +1,170 @@ +#include "bas.h" +#include "rtdb.h" +#include "geom.h" + +#include +#include + +int main() { + FILE *rtdb, *geom, *basis; + int ngen, nprim, iang; + int ncenters, sphcart, i, j; + char drivtags[20][16]; + double coords[3][20], charge[20]; + double exp[400], coeff[400]; + bool status; + double expnt_new[3] = {1.0, 2.0, 3.0}; + double coeff_new[4][3] = { + {-1.0, -2.0, -3.0}, + {0.0, -4.0, -5.0}, + {-6.0, 0.0, -7.0}, + {-8.0, -9.0, 0.0} + }; + + if (!ma_init(MT_DBL, -1, -1)) { + printf("Error initializing ma_init\n"); + return 99; + } + + status = rtdb_par_open("shit.rtdb", "unknown", &rtdb); + + printf("rtdb handle %d\n", rtdb); + + status = bas_321g_load(&rtdb); + + if (!geom_create(&geom, "321g:1-20")) { + printf("Error getting geometry handle\n"); + return 1; + } + + ncenters = 3; + // oxygen + strcpy(drivtags[0], "O"); + coords[0][0] = 0.0; + coords[1][0] = 0.0; + coords[2][0] = 0.0; + charge[0] = 8.0; + // hydrogen 1 + strcpy(drivtags[1], "H"); + coords[0][1] = 1.0; + coords[1][1] = 1.0; + coords[2][1] = 1.0; + charge[1] = 1.0; + // hydrogen 2 + strcpy(drivtags[2], "H"); + coords[0][2] = -1.0; + coords[1][2] = -1.0; + coords[2][2] = -1.0; + charge[2] = 1.0; + + if (!geom_cart_set(&geom, ncenters, drivtags, coords, charge)) { + printf("geom_cart_set fail\n"); + return 1; + } else { + status = geom_print(&geom); + } + + basis = 0; + if (!bas_create(&basis, "3211-20")) { + printf("Error getting basis handle\n"); + return 1; + } + + basis = 0; + if (!bas_create(&basis, "321g1-20")) { + printf("Error getting second basis handle\n"); + return 1; + } + + basis = 0; + if (!bas_create(&basis, "321g:1-20")) { + printf("Error getting third basis handle\n"); + return 1; + } + + status = bas_rtdb_load(&rtdb, &geom, &basis, "321g:1-20"); + status = bas_print(&basis); + status = gbs_map_print(&basis); + + status = bas_continfo(&basis, 1, false, &nprim, &ngen, &sphcart); + printf("f:query: nprim cont 1 %d\n", nprim); + printf("f:query: ngen cont 1 %d\n", ngen); + printf("f:query: sphcart cont 1 %d\n", sphcart); + + status = bas_get_exponent(&basis, 1, false, exp); + status = bas_get_coeff(&basis, 1, false, coeff); + printf("exponents and coefficients\n"); + for (i = 0; i < nprim; i++) { + for (j = 0; j < ngen; j++) { + printf("%lf ", coeff[i + j * nprim]); + } + printf("\n"); + } + + status = bas_continfo(&basis, 1, true, &nprim, &ngen, &sphcart); + printf("t:query: nprim cont 1 %d\n", nprim); + printf("t:query: ngen cont 1 %d\n", ngen); + printf("t:query: sphcart cont 1 %d\n", sphcart); + + status = bas_get_exponent(&basis, 1, true, exp); + status = bas_get_coeff(&basis, 1, true, coeff); + printf("exponents and coefficients\n"); + for (i = 0; i < nprim; i++) { + for (j = 0; j < ngen; j++) { + printf("%lf ", coeff[i + j * nprim]); + } + printf("\n"); + } + + exp[0] = 565.6589; + coeff[0] = 6.021023; + status = bas_set_exponent(&basis, 1, true, exp, nprim + 1); + status = bas_set_coeff(&basis, 1, true, coeff, nprim * ngen + 1); + status = bas_set_exponent(&basis, 1, true, exp, nprim); + status = bas_set_coeff(&basis, 1, true, coeff, nprim * ngen); + + status = bas_continfo(&basis, 1, true, &nprim, &ngen, &sphcart); + printf("modified\n"); + printf("t:query: nprim cont 1 %d\n", nprim); + printf("t:query: ngen cont 1 %d\n", ngen); + printf("t:query: sphcart cont 1 %d\n", sphcart); + + status = bas_get_exponent(&basis, 1, true, exp); + status = bas_get_coeff(&basis, 1, true, coeff); + printf("exponents and coefficients\n"); + for (i = 0; i < nprim; i++) { + for (j = 0; j < ngen; j++) { + printf("%lf ", coeff[i + j * nprim]); + } + printf("\n"); + } + + // Try adding new contractions on an existing center + printf("adding 3*3 d function on H\n"); + if (!bas_add_ucnt(basis, "H", 2, 3, 3, expnt_new, coeff_new, 4)) { + printf(" basis_add_ucnt failed"); + } + if (!bas_print(&basis)) { + printf(" print ???"); + } + + // Try adding new contractions on a new center + printf("adding 2*3 g function on Cl\n"); + if (!bas_add_ucnt(basis, "Cl", 4, 2, 3, expnt_new, coeff_new, 4)) { + printf(" basis_add_ucnt failed"); + } + if (!bas_print(&basis)) { + printf(" print ???"); + } + + printf("bas_print_all\n"); + status = bas_print_all(); + bas_err_info("who who who"); + + status = bas_high_angular(&basis, &iang); + printf("high angular momentum %d\n", iang); + status = bas_version(); + + printf("testbasis done\n"); + return 0; +} diff --git a/src/config/makefile.h b/src/config/makefile.h new file mode 100644 index 0000000..1669144 --- /dev/null +++ b/src/config/makefile.h @@ -0,0 +1,176 @@ + +# $Id: makefile.h,v 1.1.1.1 1994-03-29 06:44:24 d3g681 Exp $ + +# Common definitions for all makefiles ... these can be overridden +# either in each makefile by putting additional definitions below the +# include statement, or on the command line + + +# +# Set TOPDIR to point to your top-level directory that contains +# src, lib, config, ... (SRCDIR, etc., are derived from TOPDIR) +# + TOPDIR = /msrc/home/d3g681/allnew + SRCDIR = $(TOPDIR)/src + LIBDIR = $(TOPDIR)/lib + BINDIR = $(TOPDIR)/bin + INCDIR = $(TOPDIR)/src/include + +# +# Define TARGET to be the machine you wish to build for +# (one of SUN, IPSC, KSR) +# + TARGET = SUN + +# +# Define SUBDIRS to be list of subdirectories of SRC to be made +# +# The include directory should be first so that the include +# files are all present and correct before any compilation +# + SUBDIRS = include global db rtdb basis inp util geom input ma tcgmsg + +# +# Define LIBPATH to be paths for libraries that you are linking in +# from precompiled sources and are not building now. These libraries +# will be searched AFTER anything you are building now. +# e.g. LIBPATH = -L/msrc/proj/mss/lib +# + LIBPATH = + +# +# Define INCPATH to be directories to get includes for +# libraries that you are not building now. These directories +# will be searched AFTER anything you are building now. +# + INCPATH = + + +########################################################## +# # +# Should NOT need to modify below here unless porting to # +# a new machine or changing compiler options # +# # +########################################################## + +# !!!! Only the SUN version is up to date !!!!! + +ifeq ($(TARGET),SUN) +# +# Sun running SunOS +# + FC = f77 + CC = gcc + AR = ar + RANLIB = ranlib + SHELL = /bin/sh + MAKE = make + MAKEFLAGS = -j 2 + INSTALL = echo $@ is built + + FOPT = -g -u -Nl99 + FOPT_REN = $(FOPT) + COPT = -g + FLDOPT = $(FOPT) + CLDOPT = $(COPT) + INCLUDES = -I. $(LIB_INCLUDES) -I$(INCDIR) $(INCPATH) + WARNINGS = -Wall +#-Wshadow -Wcast-qual -Wwrite-strings -Wpointer-arith + DEFINES = -DSUN $(LIB_DEFINES) + FFLAGS = $(FOPT) $(INCLUDES) $(DEFINES) + CFLAGS = $(COPT) $(INCLUDES) $(DEFINES) $(WARNINGS) + ARFLAGS = rcv + + LIBS = -L$(LIBDIR) $(LIBPATH) \ + -linput -lgeom -lbasis -lutil -lglobal -lrtdb -ldb -linp \ + -lutil -lma -ltcgmsg + + EXPLICITF = FALSE +endif + +ifeq ($(TARGET),IPSC) +# +# DELTA/IPSC running NX +# + FC = if77 + CC = icc + CPP = /usr/lib/cpp + AR = ar860 + + RANLIB = echo + SHELL = /bin/sh + INSTALL = rcp $@ delta2: + FOPT = -O2 -Knoieee -Mquad -node -Minline=100 + FOPT_REN = -O2 -Knoieee -Mquad -Mreentrant -Mrecursive -node + COPT = -O2 -Knoieee -Mreentrant -node + INCLUDES = -I. -I$(SRCDIR)/rtdb -I$(SRCDIR)/global -I$(SRCDIR)/tcgmsg -I$(SRCDIR)/ints \ + -I$(SRCDIR)/util -I$(SRCDIR)/ma -I$(SRCDIR)/db -I$(SRCDIR)/tcgmsg/ipcv4.0 + DEFINES = -DNX -DIPSC -DNO_BCOPY $(LIB_DEFINES) +# -DGA_TRACE + FFLAGS = $(FOPT) + CFLAGS = $(COPT) $(INCLUDES) $(DEFINES) + MAKEFLAGS = -j 2 + FLDOPT = $(FOPT) -node + CLDOPT = $(COPT) -node + ARFLAGS = rcv + LIBS = $(SRCDIR)/input/libinput.a \ + $(SRCDIR)/ddscf/libddscf.a \ + $(SRCDIR)/ints/libints.a \ + $(SRCDIR)/rtdb/librtdb.a \ + $(SRCDIR)/db/libdb.a \ + $(SRCDIR)/global/libglobal.a \ + $(SRCDIR)/trace/libtrace.a \ + $(SRCDIR)/tcgmsg/ipcv4.0/libtcgmsg.a \ + $(SRCDIR)/util/libutil.a \ + $(SRCDIR)/ma/libma.a \ + $(SRCDIR)/peigs1.0/libpeigs.a \ + $(SRCDIR)/peigs1.0/liblapack.a \ + -lkmath + + EXPLICITF = TRUE +endif + + +ifeq ($(TARGET),IBM) +# +# IBM AIX .... NOT YET TESTED !!!!! +# +# FC = xlf +# CC = xlc +# AR = ar +# RANLIB = ranlib +# INSTALL = echo +# SHELL = /bin/sh +# FOPT = -g +# COPT = -g +# INCLUDES = -I. -I../ma +# DEFINES = -DTCGMSG +# FFLAGS = -qEXTNAME $(FOPT) +# FLDOPT = $(FOPT) -b rename:.exit_,.exit +# CFLAGS = $(COPT) $(INCLUDES) $(DEFINES) +# CLDOPT = $(COPT) +# ARFLAGS = rcv +# LIBS = ../tcgmsg/ipcv4.0/libtcgmsg.a ../ma/libma.a -lc +# EXPLICITF = TRUE +# +endif + +ifeq ($(EXPLICITF),TRUE) +# +# Needed on machines where FCC does not preprocess .F files +# with CPP to get .f files +# +.SUFFIXES: +.SUFFIXES: .o .s .F .f .c + +.F.o: + $(MAKE) $*.f + $(FC) -c $(FFLAGS) $*.f + /bin/rm -f $*.f + +.F.f: + $(CPP) $(INCLUDES) $(DEFINES) < $*.F | sed '/^#/D' > $*.f + +.c.o: + $(CC) $(CFLAGS) -c $*.c +endif \ No newline at end of file diff --git a/src/config/makelib.h b/src/config/makelib.h new file mode 100644 index 0000000..098a434 --- /dev/null +++ b/src/config/makelib.h @@ -0,0 +1,59 @@ +# $Id: makelib.h,v 1.1.1.1 1994-03-29 06:44:24 d3g681 Exp $ + +# +# A makefile for a library should +# +# 1) include ../config/makefile.h ... amoung other things this will +# define TARGET from which any machine dependent actions are driven +# 2) define LIBRARY as the name of the library to be made +# 3) define OBJ as the list of object files to be made +# 4) define HEADERS as the list of header/include files to be exported +# into the common include directory +# 5) optionally define LIB_TARGETS as any additional files made in +# this subdirectory that may need cleaning up +# 6) optionally define LIB_DEFINES as any additional defines for +# the C preprocessor +# 7) optionally define LIB_INCLUDES as any additional includes +# 8) include ../config/makelib.h +# 9) define any additional targets (e.g., test programs) +# +# E.g. +# +# include ../config/makefile.h +# +# OBJ = a.o b.o c.o +# LIBRARY = libsimple.a +# HEADERS = simple.h +# LIB_TARGETS = test.o test.x +# LIB_DEFINES = -DGOODBYE="\"Have a nice day\"" +# LIB_INCLUDES = -I../testdir +# +# include ../config/makelib.h +# +# test: test.o $(LIBRARY) +# $(CC) -o $@ $^ +# +# a.o b.o c.o test.o: simple.h +# + +$(LIBRARY): $(OBJ) + /bin/rm -f $@ + $(AR) $(ARFLAGS) $@ $(OBJ) + $(RANLIB) $@ + cp -p $(LIBRARY) $(LIBDIR) + +ifdef HEADERS +include_stamp: $(HEADERS) + cp -p $(HEADERS) $(INCDIR) + touch include_stamp +else +include_stamp: + touch include_stamp +endif + +clean: + /bin/rm -f $(LIBRARY) $(OBJ) core include_stamp $(LIB_TARGETS) + + +realclean: clean + /bin/rm -f *~ \#*\# \ No newline at end of file diff --git a/src/geom/GNUmakefile b/src/geom/GNUmakefile new file mode 100644 index 0000000..589cb80 --- /dev/null +++ b/src/geom/GNUmakefile @@ -0,0 +1,9 @@ + + OBJ = geom.o geom_input.o + LIBRARY = libgeom.a + HEADERS = geom.h geomP.h + +include ../config/makefile.h +include ../config/makelib.h + +geom_input.o geom.o: geomP.h diff --git a/src/geom/geom.c b/src/geom/geom.c new file mode 100644 index 0000000..f9d5a96 --- /dev/null +++ b/src/geom/geom.c @@ -0,0 +1,683 @@ +#include +#include +#include +#include + +#include "inp.h" +#include "rtdb.h" +#include "util.h" +#include "geomP.h" +#include "tcgmsg.h" +#include "context.h" + +int ngeom_rtdb = 0; +bool active[max_geom] = {false}; +char *symbols = { + "H ", "He", "Li", "Be", "B ", "C ", "N ", "O ", "F ", "Ne", + "Na", "Mg", "Al", "Si", "P ", "S ", "Cl", "Ar", "K ", "Ca", + "Sc", "Ti", "V ", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", + "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y ", "Zr", + "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", + "Sb", "Te", "I ", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", + "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", + "Lu", "Hf", "Ta", "W ", "Re", "Os", "Ir", "Pt", "Au", "Hg", + "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", + "Pa", "U ", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", + "Md", "No", "Lr" +}; + +char *elements = { + "Hydrogen", "Helium", "Lithium", "Beryllium", "Boron", + "Carbon", "Nitrogen", "Oxygen", "Fluorine", "Neon", "Sodium", + "Magnesium", "Aluminium", "Silicon", "Phosphorous", + "Sulphur", "Chlorine", "Argon", "Potassium", "Calcium", + "Scandium", "Titanium", "Vanadium", "Chromium", "Manganese", + "Iron", "Cobalt", "Nickel", "Copper", "Zinc", "Gallium", + "Germanium", "Arsenic", "Selenium", "Bromine", "Krypton", + "Rubidium", "Strontium", "Yttrium", "Zirconium", "Niobium", + "Molybdenum", "Technetium", "Ruthenium", "Rhodium", + "Palladium", "Silver", "Cadmium", "Indium", "Tin", + "Antinomy", "Tellurium", "Iodine", "Xenon", "Caesium", + "Barium", "Lanthanum", "Cerium", "Praseodymium", "Neodymium", + "Promethium", "Samarium", "Europium", "Gadolinium", + "Terbium", "Dysprosium", "Holmium", "Erbium", "Thulium", + "Ytterbium", "Lutetium", "Hafnium", "Tantalum", "Tungsten", + "Rhenium", "Osmium", "Iridium", "Platinum", "Gold", + "Mercury", "Thallium", "Lead", "Bismuth", "Polonium", + "Astatine", "Radon", "Francium", "Radium", "Actinium", + "Thorium", "Protoactinium", "Uranium", "Neptunium", + "Plutonium", "Americium", "Curium", "Berkelium", + "Californium", "Einsteinium", "Fermium", "Mendelevium", + "Nobelium", "Lawrencium" +}; + +bool geom_check_handle(FILE *geom, char *msg) { + + bool ret_val; + + ret_val = geom > 0 && geom < max_geom; + if (ret_val) ret_val = ret_val && active[geom]; + + if (!ret_val) { + printf("%s: geometry handle invalid %d", msg, geom); + geom_err_info(msg); + } + + return ret_val; +} + +bool geom_check_cent(FILE *geom, char *msg, int icent) { + bool ret_val; + ret_val = icent > 0 && icent <= ncenter[geom]; + if (!ret_val) { + printf("%s: icent invalid %d %s\n", msg, icent, names[geom]); + geom_err_info(msg); + geom_print(geom); + } + return ret_val; +} + +bool geom_rtdb_in(FILE *rtdb) { + + /* + load in info about known geometries ... this is more + for diagnostic and debugging purposes + */ + FILE *geom; + bool ret_val = false; + int ngeom_rtdb = 0; + + if (rtdb_par_get(rtdb, "geometry:ngeom", MT_INT, 1, &ngeom_rtdb)) { + if (!rtdb_par_cget(rtdb, "geometry:names", max_geom, names_rtdb)) { + printf("geom_rtdb_in: rtdb corrupt\n"); + } else { + for (geom = 0; geom < ngeom_rtdb; geom++) { + lenr[geom] = inp_strlen(names_rtdb[geom]); + } + ret_val = true; + } + } + + return ret_val; +} + +bool geom_rtdb_out(FILE *rtdb) { + + bool ret_val; + + // output to rtdb info about known geometries + + ret_val = rtdb_par_put(rtdb, 'geometry:ngeom', MT_INT, 1, ngeom_rtdb) + && rtdb_par_cput(rtdb, 'geometry:names', max_geom, names_rtdb); + if (!ret_val) printf(" geom_rtdb_out: rtdb is corrupt "); + +} + +bool geom_rtdb_add(FILE *rtdb, char *name) { + FILE *geom; + bool status, ret_val; + int ln; + + // See if name is on the rtdb already + ln = strlen(name); + status = geom_rtdb_in(rtdb); + ret_val = true; + for (geom = 0; geom < ngeom_rtdb; geom++) { + if (strncmp(name, names_rtdb[geom], ln) == 0) { + return true; + } + } + + // Name is not present ... add and rewrite info + if (ngeom_rtdb == max_geom_rtdb) { + printf(" geom_rtdb_add: too many geometries on rtdb %s\n", name); + return false; + } + + ngeom_rtdb++; + strncpy(names_rtdb[ngeom_rtdb], name, ln); + lenr[ngeom_rtdb] = ln; + + if (!geom_rtdb_out(rtdb)) { + printf(" geom_rtdb_add: rtdb error adding %.*s\n", ln, name); + return false; + } + + return true; +} + +bool geom_err_info(char *info) { + FILE *geom; + int ngeom = 0; + /* + For internal use of the geom routines only: print out + info of known geometries to aid in diagnosing a problem + */ + for (geom = 0; geom < max_geom; geom++) { + if (active[geom]) { + ngeom++; + } + } + + printf(" %s: open geometries: %d\n", info, ngeom); + + ngeom = 0; + for (geom = 0; geom < max_geom; geom++) { + if (active[geom]) { + printf(" %d %s: \"%s\" -> \"%s\"\n", ngeom, info, names[geom], trans[geom]); + } + } + + if (ngeom_rtdb > 0) { + printf(" %s: geometries in last accessed data base: %d\n", info, ngeom_rtdb); + for (geom = 0; geom < ngeom_rtdb; geom++) { + printf(" %s\n", names_rtdb[geom]); + } + } + + return true; +} + +bool geom_rtdb_load(FILE *rtdb, FILE *geom, char *name) { + char tmp[256]; + int k; + bool status, ret_val; + + ret_val = geom_check_handle(geom, "geom_rtdb_load"); + if (!ret_val) return false; + status = geom_rtdb_in(rtdb); + + // Translate the provided name + strcpy(names[geom], name); + lenn[geom] = strlen(name); + strcpy(trans[geom], "junk"); + if (!context_rtdb_match(rtdb, name, trans[geom])) + strcpy(trans[geom], name); + lent[geom] = strlen(trans[geom]); + + // Now get the info from the data base + strcpy(tmp, "geometry:"); + strncat(tmp, trans[geom], lent[geom]); + k = strlen(tmp) + 1; + status = true; + + strcpy(tmp + k, ":ncenter"); + status = status && rtdb_par_get(rtdb, tmp, MT_INT, 1, &ncenter[geom]); + strcpy(tmp + k, ":coords"); + status = status && rtdb_par_get(rtdb, tmp, MT_DBL, max_cent * 3, &coords[1][1][geom]); + strcpy(tmp + k, ":charges"); + status = status && rtdb_par_get(rtdb, tmp, MT_DBL, max_cent, &charge[1][geom]); + strcpy(tmp + k, ":efield"); + status = status && rtdb_par_get(rtdb, tmp, MT_DBL, 3, &efield[1][geom]); + strcpy(tmp + k, ":latvec"); + status = status && rtdb_par_get(rtdb, tmp, MT_DBL, 9, &latvec[1][1][geom]); + strcpy(tmp + k, ":tags"); + status = status && rtdb_par_cget(rtdb, tmp, max_cent, &tags[1][geom]); + + if (!status) { + printf(" geom_rtdb_load: not found or rtdb corrupt: %.*s -> %.*s\n", lenn[geom], names[geom], lent[geom], trans[geom]); + geom_err_info("geom_rtdb_load"); + return false; + } + + // Determine if system is periodic or if external fields are applied + oefield[geom] = ddot(3, efield[1][geom], 1, efield[1][geom], 1) > 0.0; + operiodic[geom] = ddot(9, latvec[1][1][geom], 1, latvec[1][1][geom], 1) > 0.0; + + // Compute effective nuclear repulsion energy, dipole and interaction with external fields + geom_compute_values(geom); + + active[geom] = true; + return true; +} + +double geom_compute_values(FILE *geom) { + /* + compute effective nuclear repulsion energy, dipole and + interaction with external fields + */ + + double e, r; + int i, j; + + e = 0.0; + ndipole[0][geom] = 0.0; + ndipole[1][geom] = 0.0; + ndipole[2][geom] = 0.0; + + // compute nuclear dipole moment and usual nuclear repulsion energy + for (i = 0; i < ncenter[geom]; i++) { + for (j = 0; j < 3; j++) { + ndipole[j][geom] += charge[i][geom] * coords[j][i][geom]; + } + for (j = i + 1; j < ncenter[geom]; j++) { + r = sqrt(pow(coords[0][i][geom] - coords[0][j][geom], 2) + + pow(coords[1][i][geom] - coords[1][j][geom], 2) + + pow(coords[2][i][geom] - coords[2][j][geom], 2)); + e += charge[i][geom] * charge[j][geom] / r; + } + } + + // add in interaction of nuclear dipole with external field + e += ddot(3, ndipole[0][geom], 1, efield[0][geom], 1); + + erep[geom] = e; +} + +bool geom_rtdb_store(FILE *rtdb, char *name, FILE *geom) { + bool status, ret_val; + char tmp[256]; + + ret_val = geom_check_handle(geom, "geom_rtdb_store"); + if (!ret_val) { + return false; + } + + // Update the name if provided + if (name != NULL && strcmp(name, "") != 0) { + strcpy(names[geom], name); + lenn[geom] = strlen(name); + } + + // If not process 0 return ... this is so that input routines can be completely single threaded + if (nodeid() != 0) { + return true; + } + + // Try to translate the name + strcpy(trans[geom], "junk"); + if (!context_rtdb_match(rtdb, name, trans[geom])) { + strcpy(trans[geom], name); + } + lent[geom] = strlen(trans[geom]); + + // Now put the info into the data base + strcpy(tmp, "geometry:"); + k = strlen(tmp); + status = true; + + strcpy(tmp[k], ":ncenter\0"); + status = status && rtdb_par_put(rtdb, tmp, MT_INT, 1, &ncenter[geom]); + strcpy(tmp[k], ":coords\0"); + status = status && rtdb_par_put(rtdb, tmp, MT_DBL, ncenter[geom] * 3, &coords[1][1][geom]); + strcpy(tmp[k], ":charges\0"); + status = status && rtdb_par_put(rtdb, tmp, MT_DBL, ncenter[geom], &charge[1][geom]); + strcpy(tmp[k], ":efield\0"); + status = status && rtdb_par_put(rtdb, tmp, MT_DBL, 3, &efield[1][geom]); + strcpy(tmp[k], ":latvec\0"); + status = status && rtdb_par_put(rtdb, tmp, MT_DBL, 9, &latvec[1][1][geom]); + strcpy(tmp[k], ":tags\0"); + status = status && rtdb_par_cput(rtdb, tmp, ncenter[geom], &tags[1][geom]); + + // Insert translated name into list of known geometries + status = status && geom_rtdb_add(rtdb, name); + + // Check that all rtdb operations were successful + if (!status) { + printf(" geom_rtdb_store: write to rtdb failed: %.*s -> %.*s\n", lenn[geom], names[geom], lent[geom], trans[geom]); + geom_err_info("geom_rtdb_store"); + return false; + } + + return true; +} + +bool geom_rtdb_delete(FILE *rtdb, char *name) { + char translation[256], tmp[256]; + int lt, geom, geom2, k; + bool status, set_true = false; + + // try to translate the provided name + if (rtdb_par_cget(rtdb, name, 1, translation) != 0) { + strcpy(translation, name); + } + lt = strlen(translation); + + // locate name in list and remove + status = geom_rtdb_in(rtdb); + for (geom = 1; geom <= ngeom_rtdb; geom++) { + if (strncmp(names_rtdb[geom], translation, lt) == 0) { + set_true = true; + break; + } + } + + if (!set_true) { + printf(" geom_rtdb_delete: no such geometry %.*s -> %.*s\n", strlen(name), name, lt, translation); + } + + for (geom2 = geom + 1; geom2 <= ngeom_rtdb; geom2++) { + strcpy(names_rtdb[geom2 - 1], names_rtdb[geom2]); + } + ngeom_rtdb--; + + status = geom_rtdb_out(rtdb); + + // delete each entry associated with a geometry in the database + strcpy(tmp, "geometry:"); + k = strlen(tmp); + + strcpy(tmp[k], ":ncenter"); + status = status && rtdb_par_delete(rtdb, tmp); + strcpy(tmp[k], ":coords"); + status = status && rtdb_par_delete(rtdb, tmp); + strcpy(tmp[k], ":charges"); + status = status && rtdb_par_delete(rtdb, tmp); + strcpy(tmp[k], ":efield"); + status = status && rtdb_par_delete(rtdb, tmp); + strcpy(tmp[k], ":latvec"); + status = status && rtdb_par_delete(rtdb, tmp); + strcpy(tmp[k], ":tags"); + status = status && rtdb_par_delete(rtdb, tmp); + + // check status of all rtdb stores + if (!status) { + printf(" geom_rtdb_delete: rtdb corrupt %.*s\n", lt, translation); + geom_err_info("geom_rtdb_delete"); + return false; + } + + return true; +} + +bool geom_create(FILE *geom, char *name) { + char translation[256]; + int i; + + // Assign the next free slot for a geometry + for (i = 0; i < max_geom; i++) { + if (!active[i]) { + break; + } + } + + if (i == max_geom) { + printf("geom_create: too many geoms trying to create %s\n", name); + geom_err_info("geom_create"); + return false; + } + + // Store info about the geometry + strcpy(names[i], name); + strcpy(trans[i], " "); + lenn[i] = strlen(name); + ncenter[i] = 0; + active[i] = true; + + return true; +} + +bool geom_destroy(FILE *geom) { + + bool ret_val; + bool ret_val = geom_check_handle(geom, "geom_destroy"); + if (!ret_val) return false; + + active[geom] = false; + + return true; +} + +bool geom_cart_set(FILE *geom, int ncent, char *t[], double c[3][ncent], double q[ncent]) { + + int i; + bool ret_val; + + if (!geom_check_handle(geom, "geom_cart_set")) { + return false; + } + + if (ncent <= 0 || ncent > max_cent) { + printf("geom_cart_set: too many centers %d %s\n", ncent, names[geom]); + return false; + } + + ncenter[geom] = ncent; + for (i = 0; i < ncent; i++) { + strcpy(tags[i][geom], t[i]); + charge[i][geom] = q[i]; + coords[0][i][geom] = c[0][i]; + coords[1][i][geom] = c[1][i]; + coords[2][i][geom] = c[2][i]; + } + /* + compute effective nuclear repulsion energy, dipole and + interaction with external fields + */ + geom_compute_values(geom); + + return true; +} + +bool geom_cart_get(FILE *geom, int *ncent, char *t[], double c[][ncent], double q[]) { + + int i; + + if (!geom_check_handle(geom, "geom_cart_get")) { + return false; + } + + *ncent = ncenter[geom]; + for (i = 0; i < *ncent; i++) { + strcpy(t[i], tags[i][geom]); + q[i] = charge[i][geom]; + c[0][i] = coords[0][i][geom]; + c[1][i] = coords[1][i][geom]; + c[2][i] = coords[2][i][geom]; + } + + return true; +} + +bool geom_cent_get(FILE *geom, int icent, char *t, double c[3], double *q) { + bool ret_val; + ret_val = geom_check_handle(geom, "geom_cent_get"); + if (!ret_val) return false; + ret_val = geom_check_cent(geom, "geom_cent_get", icent); + if (!ret_val) return false; + + strcpy(t, tags[icent][geom]); + c[0] = coords[0][icent][geom]; + c[1] = coords[1][icent][geom]; + c[2] = coords[2][icent][geom]; + q = charge[icent][geom]; + + return true; +} + +bool geom_cent_set(FILE *geom, int icent, char *t, double c[3], double q) { + if (!geom_check_handle(geom, "geom_cent_set")) { + return false; + } + + if (!geom_check_cent(geom, "geom_cent_set", icent)) { + return false; + } + + strcpy(tags[icent][geom], t); + coords[0][icent][geom] = c[0]; + coords[1][icent][geom] = c[1]; + coords[2][icent][geom] = c[2]; + charge[icent][geom] = q; + + geom_compute_values(geom); + + return true; +} + +bool geom_ncent(FILE *geom, int ncent) { + bool ret_val; + ret_val = geom_check_handle(geom, "geom_ncent"); + if (!ret_val) return false; + ncent = ncenter[geom]; + + return true; +} + +bool geom_cent_tag(FILE *geom, int icent, char *tag) { + if (!geom_check_handle(geom, "geom_cent_tag")) { + return false; + } + + if (!geom_check_cent(geom, "geom_cent_tag", icent)) { + return false; + } + + strcpy(tag, tags[icent][geom]); + + return true; +} + +bool geom_latvec_set(FILE *geom, double vectors[3][3]) { + errquit("geom_latvec_set: not yet!", 0); + + return false; +} + +bool geom_latvec_get(FILE *geom, double vectors[3][3]) { + errquit("geom_latvec_get: not yet!", 0); + + return false; +} + +bool geom_efield_set(FILE *geom, double efield[3]) { + errquit("geom_efield_set: not yet!", 0); + geom_set_values(geom); + + return false; +} + +bool geom_efield_get(FILE *geom, double efield) { + errquit("geom_efield_get: not yet!", 0); + + return false; + +} + +bool geom_print(FILE *geom) { + /* + Basic printing of cartesian geometry ... needs support for + user defined units, internal coords, different formats, ... + */ + + int icent, ivec, i; + bool ret_val; + + if (!geom_check_handle(geom, "geom_print")) { + return false; + } + + printf(" Geometry (au) \"%s\" -> \"%s\"\n", names[geom], trans[geom]); + printf(" -------------\n"); + printf(" No. Tag Charge X Y Z\n"); + printf(" ---- ---------------- ---------- -------------- -------------- --------------\n"); + + for (icent = 0; icent < ncenter[geom]; icent++) { + printf("%4d %16s %10.6f %14.8f %14.8f %14.8f\n", icent, tags[icent][geom], charge[icent][geom], coords[0][icent][geom], coords[1][icent][geom], coords[2][icent][geom]); + } + + printf("Effective nucler repulsion charge (au) %18.10f", erep[geom]); + + if (operiodic[geom]) { + printf("Periodic lattice vectors (au)\n"); + printf(" -----------------------------\n"); + printf(" X Y Z\n"); + printf(" ---------------- ---------------- ----------------\n"); + for (ivec = 0; ivec < 3; ivec++) { + printf(" %17.10f %17.10f %17.10f\n", latvec[ivec][0][geom], latvec[ivec][1][geom], latvec[ivec][2][geom]); + } + + } + + if (oefield[geom]) { + printf("Electric Field (au)\n"); + printf(" -------------------\n"); + printf(" X Y Z\n"); + printf(" ---------------- ---------------- ----------------\n"); + printf(" %17.10f %17.10f %17.10f\n", efield[0][geom], efield[1][geom], efield[2][geom]); + } + + return true; +} + +bool geom_tag_to_element(char *tag, char *symbol, char *element, int *atn) { + /* + attempt to figure out which element a tag refers to + and return the symbol, name and atomic no. + */ + + bool ret_val; + int lbuf, ind; + char buf[17]; + char sym1[15] = {'h', 'b', 'c', 'n', 'o', 'f', 'p', 's', 'k', 'v', 'y', 'i', 'w', 'u'}; + int atn1[14] = {1, 5, 6, 7, 8, 9, 15, 16, 19, 23, 39, 53, 74, 92}; + + ret_val = false; + /* + eliminate conventions that refer to centers used for + computation purposes .. just bq for now + */ + lbuf = strlen(buf); + if (lbuf == 0) return false; + + for (int i = 0; i < lbuf; i++) { + buf[i] = tolower(buf[i]); + } + + if (strncmp(buf, "bq", 2) == 0) { + strcpy(element, "point charge"); + strcpy(symbol, "bq"); + atn = 0; + return false; + } + /* + Attempt to match the first 4 characters of the + full names of the elements + */ + atn = 0; + if (lbuf >= 4) { + for (int i = 0; i < nelements; i++) { + if (strncmp(buf, elements[i], 4) == 0) { + strcpy(symbol, symbols[i]); + strcpy(element, elements[i]); + atn = i; + ret_val = true; + return true; + } + } + } + /* + Failed ... attempt to match the first two characters + against two character element names + */ + if (buf[1] != ' ') { + for (int i = 0; i < nelements; i++) { + if (strncmp(buf, symbols[i], 2) == 0) { + strcpy(symbol, symbols[i]); + strcpy(element, elements[i]); + atn = i; + ret_val = true; + return true; + } + } + } + + // Last ditch attempt ... match against 1 character symbols + for (int i = 0; i < 14; i++) { + if (buf[0] == sym1[i]) { + ind = atn1[i]; + strcpy(symbol, symbols[ind]); + strcpy(element, elements[ind]); + atn = ind; + ret_val = true; + return true; + } + } + + // Nothing matched + strcpy(symbol, " "); + strcpy(element, " "); + atn = 0; + return false; + +} \ No newline at end of file diff --git a/src/geom/geom.doc b/src/geom/geom.doc new file mode 100644 index 0000000..ab12b0b --- /dev/null +++ b/src/geom/geom.doc @@ -0,0 +1,113 @@ + +The geometry data includes + + 1) A description of the coordinates of all types of centers (e.g., + atom, charge, basis function) + + 2) Charges (and I guess possibly other potentials) associated with + those centers + + 3) Tags (names) of centers + + 4) Masses associated with centers + + 5) Variables for optimization (e.g., via constrained cartesians + or zmatrix variables) + + 6) Any other simple scalar/vector attributed associated + specifically with a center + +Operations + + 1) Store/retrieve from the database + + logical geom_rtdb_load(rtdb, name, geom) + integer rtdb [input] + character*(*) name [input] + integer geom [output] + + logical geom_rtdb_store(rtdb, 'geometry', geom) + integer rtdb [input] + character*(*) name [input] + integer geom [input] + + 2) Create/destroy + + logical geom_create(geom) + integer geom [output] + + logical geom_destroy(geom) + integer geom [input] + + 3) Set/get commmon values for all centers + + logical geom_cart_set(geom, ncent, tags, coords, charges) + integer geom [input] + integer ncent [input] + character*(*) tags(ncent) [input] + character*(*) coords(3, ncent) [input] + character*(*) charges(ncent) [input] + + logical geom_cart_get(geom, ncent, tags, coords, charges) + integer geom [input] + integer ncent [output] + character*(*) tags(ncent) [output] + character*(*) coords(3, ncent) [output] + character*(*) charges(ncent) [output] + + 4) Set/get common values for specific centers + + logical geom_cent_set(geom, icent, tag, coord, charge) + integer geom [input] + integer ncent [input] + character*(*) tag [input] + character*(*) coords(3) [input] + character*(*) charge [input] + + logical geom_cent_get(geom, icent, tag, coord, charge) + integer geom [input] + integer ncent [output] + character*(*) tag [output] + character*(*) coords(3) [output] + character*(*) charge [output] + + 5) Inquiry routines + + integer function geom_ncent(geom) + integer geom [input] + + logical function geom_cent_tag(geom, icent, tag) + integer geom [input] + integer icent [input] + character*(*) tag [output] + + 6) Set/get specific values for specific centers + + There are two possibilities here + + a) adopt an extensible definition of properties associated + with a center. This includes registering new properties + with a name and routines to set/get/load/store the values + and some general format (e.g., netcdf) for describing + and passing data. + + b) adopt a static definition of the data structures and + require recompilation after the structures have been changed + and new routines provided. + + Do we think that new properties will be added very regularly or + that this will become very infrequent? I tend to think the latter, + so a) is not yet worth the effort. Since b) requires very little + effort we can always change our minds and do a) later. + + + 7) Zmatrix routines ... not yet defined + + n_zmat_cent, n_zmat_vars, ... + logical geom_zmat_defined() + call geom_zmat_get + call geom_zmat_set + ... + + +Data on the rtdb diff --git a/src/geom/geom.h b/src/geom/geom.h new file mode 100644 index 0000000..1da34ee --- /dev/null +++ b/src/geom/geom.h @@ -0,0 +1,31 @@ +#ifndef _GEOM_H +#define _GEOM_H + +#include + + bool geom_check_handle(FILE *, char *); + bool geom_check_cent(FILE *, char *, int); + bool geom_rtdb_in(FILE *); + bool geom_rtdb_out(FILE *); + bool geom_rtdb_add(FILE *, char *); + bool geom_err_info(char *); + bool geom_rtdb_load(FILE *, FILE *, char *); + double geom_compute_values(FILE *); + bool geom_rtdb_store(FILE *, char *, FILE *); + bool geom_rtdb_delete(FILE *, char *); + bool geom_create(FILE *, char *); + bool geom_destroy(FILE *); + bool geom_cart_set(FILE *, int, char *[], double[3][], double[]); + bool geom_cart_get(FILE *, int *, char *[], double *[], double []); + bool geom_cent_get(FILE *, int, char *, double[3], double *); + bool geom_cent_set(FILE *, int, char *, double[3], double); + bool geom_ncent(FILE *, int); + bool geom_cent_tag(FILE *, int, char *); + bool geom_latvec_set(FILE *, double [3][3]); + bool geom_latvec_get(FILE *, double [3][3]); + bool geom_efield_set(FILE *, double[3]); + bool geom_efield_get(FILE *, double); + bool geom_print(FILE *); + bool geom_tag_to_element(char *, char *, char *, int *); + +#endif \ No newline at end of file diff --git a/src/geom/geomP.h b/src/geom/geomP.h new file mode 100644 index 0000000..c4aee15 --- /dev/null +++ b/src/geom/geomP.h @@ -0,0 +1,84 @@ +#ifndef _GEOMP_H +#define _GEOMP_H +/* + Private fortran include file for the geometry routines + + Parameters + + max_geom = maximum no. of geometries + max_cent = maximum no. of centers in a geometry + max_geom_rtdb = maximum no. of geometries stored in the rtdb + nelments = no. of elements that info is stored about + + [The only thing that cannot be dynamically allocated are the + character variables for the tags ... I was lazy and just statically + dimensioned everything ... just drudge work to dynamically + allocate though if necessary ... which it hopefully won't be + ... since only geom.F (and maybe the basis routines) include + this header file only these need to be recompiled if the parameters + are changed] + + Members of /cgeometry/ + + ngeom_rtdb = current no. of geometries on the rtdb + active(1:max_geom) = true if this geometry is open + ncenter(1:max_geom) = no. of centers in this geometry + coords(1:3,1:max_cent,1:max_geom) = cartesian coords of this geometry + charge(1:max_cent,1:max_geom) = charges associated with centers + dipole ... not yet + quadrupole ... not yet + pseudopotential ... not yet + efield(1:3,1:max_geom) = external electric field applied to this system + oefield = true if efield is on + latvec(1:3,1:3,1:max_geom) = vectors specifing periodicity + (null vector gives no periodicity) + operiodic = true if a lattice vector is non-null + erep(1:max_geom) = interaction energy of centers with each other + and external fields. At its simplest this is + just the nuclear repulsion energy + ndipole(1:3,1:max_geom) = nuclear dipole moment + Members of /ccgeometry/ + + names(1:max_geom) = names of open geometries + trans(1:max_geom) = translations of names of open geoms + names_rtdb(1:max_geom) = names of geometries in the rtdb + tag(1:max_cent,1:max_geom) = tags associated with centers + lenn(1:max_geom) = length of names(geom) minus trailing blanks + lent(1:max_geom) = length of trans(geom) ... + lenr(1:max_geom) = length of names_rtdb(geom) ... + symbols(1:nelements) = symbols for elements + elements(1:nelements) = names of elements +*/ + +#define MAX_GEOM 2 +#define MAX_CENT 1000 +#define MAX_GEOM_RTDB 100 +#define NELEMENTS 103 + +typedef struct { + double coords[3][MAX_CENT][MAX_GEOM]; + double charge[MAX_CENT][MAX_GEOM]; + double efield[3][MAX_GEOM]; + double latvec[3][3][MAX_GEOM]; + double erep[MAX_GEOM]; + double ndipole[3][MAX_GEOM]; + int ncenter[MAX_GEOM]; + int active[MAX_GEOM]; + int lenn[MAX_GEOM]; + int lent[MAX_GEOM]; + int lenr[MAX_GEOM]; + int operiodic[MAX_GEOM]; + int oefield[MAX_GEOM]; + int ngeom_rtdb; +} CGeometry; + +typedef struct { + char names[MAX_GEOM][256]; + char trans[MAX_GEOM][256]; + char names_rtdb[MAX_GEOM_RTDB][256]; + char tags[MAX_CENT][MAX_GEOM][16]; + char symbols[NELEMENTS][2]; + char elements[NELEMENTS][16]; +} CCGeometry; + +#endif // _GEOMP_H diff --git a/src/geom/geom_input.c b/src/geom/geom_input.c new file mode 100644 index 0000000..93ef968 --- /dev/null +++ b/src/geom/geom_input.c @@ -0,0 +1,98 @@ +#include +#include + +#include "inp.h" +#include "geom.h" +#include "tcgmsg.h" + +void geom_input(FILE *rtdb, bool print) { + char field[255]; // for character input + char name[255]; // for name of geometry + char units[12]; // holds units of coordinates + int ncenter; // counts no. of centers as input + FILE *geom; // handle for geometry + bool status; // scratch for return codes + const int max_center = 1000; // parameter for local array dimension + double coords[max_center][3]; + double charge[max_center]; + char tags[max_center][16]; + /* + read a geometry from the input deck and output it + to the rtdb. + + current input line should begin 'geometry ...' + + Cartesians only for now + */ + if (nodeid() != 0) return; + + // Check that this is indeed a geometry line + inp_set_field(0); // goto start of line + if (!inp_a(field)) { + errquit("geom_input: no input present", 0); + } + if (!inp_compare(false, "geom", field)) { + errquit("geom_input: not geometry input", 0); + } + + // geometry [] [units ] + strcpy(units, "atomic units"); + strcpy(name, " "); + while (inp_a(field)) { + if (inp_compare(false, "units", field)) { + if (!inp_a(units)) { + errquit("geom_input: geometry [] [units ]", 0); + } + geom_check_units(units); + } else { + if (strcmp(name, " ") != 0) { + errquit("geom_input: geometry [] [units ]", 0); + } + strcpy(name, field); + } + } + + if (!geom_create(geom, name)) { + errquit("geom_input: geom_create failed !", 0); + } + + // tag charge x y z + ncenter = 0; + while (inp_read()) { + status = inp_a(field); + if (inp_compare(false, "end", field)) break; + + else { + if ((ncenter + 1) == max_center) + errquit("geom_input: too many centers?", ncenter); + strcpy(tags[ncenter + 1], field); + status = status && inp_f(charge[ncenter + 1]); + status = status && inp_f(coords[0][ncenter + 1]); + status = status && inp_f(coords[1][ncenter + 1]); + status = status && inp_f(coords[2][ncenter + 1]); + if (!status) + errquit("geom_input: ", 0); + ncenter++; + } + } + + if (!geom_cart_set(geom, ncenter, tags, coords, charge)) { + errquit("geom_input: geom_cart_set failed", 0); + } + + if (print) { + if (!geom_print(geom)){ + errquit("geom_input: print failed ", 0); + } + } + + if (!geom_rtdb_store(rtdb, name, geom)) { + errquit("geom_input: geom_rtdb_store failed", 0); + } + + if (!geom_destroy(geom)) { + errquit("geom_input: geom_destroy failed", 0); + } + + // done +} diff --git a/src/include/GNUmakefile b/src/include/GNUmakefile new file mode 100644 index 0000000..0548e7d --- /dev/null +++ b/src/include/GNUmakefile @@ -0,0 +1,20 @@ +# +# This directory is a central repository for all include +# files. The makefile in each subdirectory should contain +# a rule that keeps this directory up to date +# + +include ../config/makefile.h + +includes: + for dir in $(SUBDIRS); do \ + echo Making include_stamp in $(SRCDIR)/$$dir ; \ + (cd $(SRCDIR)/$$dir; $(MAKE) include_stamp) ; \ + done + +include_stamp: + echo Nothing to be done + +realclean clean: + echo Header files not removed + /bin/rm -f *~ \#*\# \ No newline at end of file diff --git a/src/inp/GNUmakefile b/src/inp/GNUmakefile new file mode 100644 index 0000000..94c090a --- /dev/null +++ b/src/inp/GNUmakefile @@ -0,0 +1,13 @@ +# $Id: GNUmakefile,v 1.1.1.1 1994-03-29 06:44:37 d3g681 Exp $ + + OBJ = inp.o + LIBRARY = libinp.a + LIB_TARGETS = test.o test + HEADERS = inp.fh + + +include ../config/makefile.h +include ../config/makelib.h + +test: test.o input.o + $(FC) $(FFLAGS) -o $@ $^ $(LIBS) diff --git a/src/inp/inp.doc b/src/inp/inp.doc new file mode 100644 index 0000000..0062062 --- /dev/null +++ b/src/inp/inp.doc @@ -0,0 +1,191 @@ + All routines are declared in the header file 'inp.h' + + + subroutine inp_init(ir, iw) + + Initialize free format input routines to take input from + fortran unit ir and send their output to fortran unit iw. + The input file is processed from the current location. + + inp_init() shuld be invoked each time the input file is + repositioned using other than inp_*() routines (e.g., rewind). + + + logical function inp_read() + + Read a line from the input and split it into white space (blank + or tab) separated fields. White space may be incorporated into a + field by enclosing it in quotes ("). The case of input is + preserved. Blank lines are ignored, and text from a pound or + hash symbol (#) to the end of the line is treated as a comment. + A backslash(\) at the end of a line (only white space may appear + after it) may be used to concatentate physical input lines into + one logical input line. A semicolon (;) may be used to split a + physical input line into multiple logical input lines. The + special meaning of hash (#), semicolon (;) and quotation (") + characters may be avoided only by prefacing them with a backslash + (this must be done even if the character is inside a quoted + character string). + + The no. of fields read is set to 0, there being a total of + inp_nfield() fields in the line. + + If a non-blank line is successfully parsed then .true. is returned. + + Otherwise an internal error message is set and .false. is returned. + + Possible errors include detection of EOF (inp_eof() may be used + to check for this condition) or failure to parse the line (e.g., + a character string without a terminating quote). + + EOF may be indicated by end of the physical input file, or by a + physical input line that begins with either asterisk (*), period + (.) or EOF (ignoring case), and has only trailing white space. + + There is a maximum input line width of 256 characters. + + + logical function inp_i(integer i) + + Attempt to read the next field as an integer. + Upon success return .true. and advance to the next field. + Otherwise return .false., save an internal error message and do + not change the current field. + + + logical function inp_f(double precision d) + + Attempt to read the next field as a floating point number. + Upon success return .true. and advance to the next field. + Otherwise return .false., save an internal error message and do + not change the current field. + + + logical function inp_a(character*(*) a) + + Attempt to read the next field as a character string. + Upon success return .true. and advance to the next field. + Otherwise return .false., save an internal error message and do + not change the current field. + + + logical function inp_a_trunc(character*(*) a) + + Attempt to read the next field as a character string, quietly + discarding any data that does not fit in the user provided buffer. + Upon success return .true. and advance to the next field. + Otherwise return .false., save an internal error message and do + not change the current field. + + logical function inp_line(character*(*) z) + character*(*) z + + Return in z as much of the entire input line as it will hold and + quietly discard any overflow. Upon success return .true., + otherwise save an internal error message and return .false. + + integer function inp_n_field() + + Returns the no. of fields in the current input line (1, ...). A + value of 0 implies either that EOF or some other error was + detected or inp_read() has not yet been called. + + integer function inp_cur_field() + + Returns the no. of fields in the input line that have been + processed so far (0, ...). Thus if inp_cur_field() returns 2, + then the next field read by inp_f() etc. will be field 3. + + subroutine inp_set_field(value) + integer value + + Sets the current field (as returned by inp_cur_field) to be + value. 0 <= value <= inp_n_field(). An out of range value + results in error termination. + + + subroutine inp_prev_field() + + A convenience routine that positions you to read the field (on + the current input line) that was last read. It is simply + implemented as + + call inp_set_field(max(0,inp_cur_field()-1)) + + At the beginning of the line this is a null operation. + + + logical function inp_compare(ocase, a, b) + logical ocase + character*(*) a, b + + Return .true. iff all the characters in A match the first + len(A) characters of B. If ocase is .true. then comparisons are + case sensitive, otherwise comparisons ignore case. + + + logical function inp_match(nrec, ocase, test, array, ind) + integer nrec + logical ocase + character*(*) test + character*(*) array(nrec) + integer ind + + Let L be the length of the character string test ignoring + trailing blanks. Attempt to find a unique match of test(1:L) + against elements of array(*). If ocase is .true. then + comparisons are case sensitive, otherwise comparisons ignore + case. + + If a unique match is made return the index of the element in ind + and return .true. + + If the match is ambiguous set ind to 0, and return .false. + + If no match is found set ind to -1 and return .false. + + + logical function inp_search(ocase, z) + character*(*) z + logical ocase + + Position the input file at the next logical input line which has + a first input field that matches the leading non-blank characters + in z. If ocase is .true. then matches are case sensitive. + + If such a line is found then return .true., and reset the current + input field to 0 (i.e., as if inp_read() had just been called). + + If no such line is found return .false.. The file will be either + at EOF or at a line which was not successfully parsed. EOF may + be detected by inp_eof(). + + + logical function inp_eof() + + Return .true. if EOF has been detected, .false. otherwise. + + + subroutine inp_lcase(z) + character*(*) z + + Lowercase the character string z + + + integer function inp_strlen(z) + character*(*) z + + Return the index of the last non-blank character in z, 0 being + returned for a fully blank string. + + + subroutine inp_errout() + + If there is an internal error message, print out its value, + the current line number and its contents. If appropriate + indicate the problematic position in the current input line. + + + subroutine inp_outrec() + + Print out the current input line. \ No newline at end of file diff --git a/src/inp/inp.h b/src/inp/inp.h new file mode 100644 index 0000000..d86cb78 --- /dev/null +++ b/src/inp/inp.h @@ -0,0 +1,18 @@ +#ifndef _INP_H +#define _INP_H + + int inp_i(); + float inp_f(); + char *inp_a(); + int inp_n_field(); + int inp_cur_field(); + int inp_match(); + int inp_read(); + int inp_search(); + int inp_compare(); + int inp_strlen(); + int inp_line(); + int inp_eof(); + int inp_a_trunc(); + +#endif \ No newline at end of file diff --git a/src/inp/inpP.h b/src/inp/inpP.h new file mode 100644 index 0000000..0ddece8 --- /dev/null +++ b/src/inp/inpP.h @@ -0,0 +1,34 @@ +#ifndef _INPP_H +#define _INPP_H + +// Private header file for free format input routines + +#include + + #define MAX_WIDTH 256 // Maximum no. of characters in an input line + #define MAX_FIELD MAX_WIDTH/2 + 1 // Maximum no. of fields in an input line + char ja[256]; // Input buffers ... MUST match max_width + char tmp[256]; // Same size work space + char errmsg[80]; // Error message + char xcomm; // Comment character + char xsplit; // Character to split physical input lines + char xback; // Backslash for concatenation and quoting + char xquote; // Quotation marks for strings + char xblnk; // Space + char xtab; // Tab + + int jrec; // No. of current field + int jump; // No. of fields in current line + int istrt[MAX_FIELD]; // Start of fields + int inumb[MAX_FIELD]; // Length of fields + int nstart[MAX_FIELD]; // Start of fields + int nend[MAX_FIELD]; // End of fields + int iwidth; // Length of current logical input line + int nline; // Current logical line inside physical line + int noline; // No. of logical lines inside physical line + int input_line; // No. of current physical input line + int nerr; // ???? + bool oswit; // True if EOF has beeen detected + int ierrpos; // Input char position where error was detected + +#endif // _INPP_H diff --git a/src/inp/test.c b/src/inp/test.c new file mode 100644 index 0000000..cc2020c --- /dev/null +++ b/src/inp/test.c @@ -0,0 +1,36 @@ +#include + +#include "inp.h" + +void test() { + char aval[30]; + int i, ival, line; + double dval; + + line = 0; + inp_init(5, 6); + + while (inp_read()) { + line = line + 1; + inp_outrec(); + for (i = 1; i <= inp_n_field(); i++) { + if (inp_i(&ival)) { + printf("line=%d, field=%d, integer=%d\n", line, i, ival); + } else if (inp_f(&dval)) { + printf("line=%d, field=%d, double=%.2lf\n", line, i, dval); + } else if (inp_a(aval)) { + printf("line=%d, field=%d, string=%s\n", line, i, aval); + } else { + printf("line=%d, field=%d, error!\n", line, i); + inp_errout(); + } + } + } + + if (inp_eof()) { + printf("EOF detected at line %d\n", line); + } else { + printf("input failed at line %d\n", line); + } + inp_errout(); +} diff --git a/src/rtdb/GNUmakefile b/src/rtdb/GNUmakefile new file mode 100644 index 0000000..084eacd --- /dev/null +++ b/src/rtdb/GNUmakefile @@ -0,0 +1,47 @@ +# $Id: GNUmakefile,v 1.1.1.1 1994-03-29 06:44:27 d3g681 Exp $ + +include ../config/makefile.h + + OBJ = rtdb_f2c.o rtdb.o rtdb_par.o rtdb_par_f2c.o \ + context.o context_f2c.o + LIBRARY = librtdb.a + + HEADERS = context.h rtdb.h rtdb.h context.h + + LIB_TARGETS = test test.o rtdbtest rtdbtest.o interact context davetest \ + context.o davetest.o interact.o rtdb_par_f2c.o \ + cntx.o cntx + + LIB_INCLUDES = -I../db + + TEST_LIBS = $(LIBRARY) $(LIBS) + +include ../config/makelib.h + +davetest: davetest.o $(LIBRARY) + $(FC) $(FFLAGS) -o $@ davetest.o librtdb.a ../db/libdb.a ../util/libutil.a ../ma/libma.a + +rtdb_par_f2c.c: rtdb_f2c.c + sed 's/rtdb_/rtdb_par_/g' rtdb_f2c.c > rtdb_par_f2c.c + +cntx: cntx.o $(LIBRARY) + $(FC) $(FFLAGS) -o $@ cntx.o $(LIBS) + +interact: interact.o $(LIBRARY) + $(CC) $(CFLAGS) -o $@ interact.o $(TEST_LIBS) + +test: test.o $(LIBRARY) + $(FC) $(FFLAGS) -o $@ test.o $(TEST_LIBS) + +rtdbtest: rtdbtest.o $(LIBRARY) + $(CC) $(CFLAGS) -o $@ rtdbtest.o $(TEST_LIBS) + +rtdbpartest: rtdb_par_test.o $(LIBRARY) + $(CC) $(CFLAGS) -o $@ rtdb_par_test.o $(TEST_LIBS) + +rtdb.o rtdbf2c.o rtdbtest.o: misc.h +rtdb.o rtdbf2c.o rtdbtest.o: rtdb.h +test.o: rtdb.h + +context: context.o $(LIBRARY) + $(CC) $(CFLAGS) -o $@ context.o $(TEST_LIBS) diff --git a/src/rtdb/context.h b/src/rtdb/context.h new file mode 100644 index 0000000..0e5deda --- /dev/null +++ b/src/rtdb/context.h @@ -0,0 +1,15 @@ +#ifndef _CONTEXT_H +#define _CONTEXT_H + +#include + +bool context_set(const char *); +char *context_get(void); +bool context_rtdb_store(int); +bool context_rtdb_load(int); +bool context_push(const char *); +bool context_pop(const char *); +bool context_rtdb_match(int, const char *, int, char *); +bool context_prefix(const char *, char *, int); + +#endif \ No newline at end of file diff --git a/src/rtdb/rtdb.h b/src/rtdb/rtdb.h new file mode 100644 index 0000000..fd015aa --- /dev/null +++ b/src/rtdb/rtdb.h @@ -0,0 +1,154 @@ +#ifndef _RTDB_H +#define _RTDB_H + +/* + All routines return TRUE (1) on success, FALSE (0) on failure. + + int rtdb_open(const char *filename, const char *mode, int *handle) + + Filename = path to file associated with the data base + mode = 'new' Open only if it does not exist already + 'old', Open only if it does exist already + 'unknown' Create new or open existing (preserving contents) + 'empty' Create new or open existing (deleting contents) + 'scratch' Create new or open existing (deleting contents) + and automatically delete upon closing. Also, items + cached in memory are not written to disk. + + handle = returns handle by which all future references to the + data base are made + + + + int rtdb_close(const int handle, const char *mode) + + Close the data base + + handle = handle to RTDB + mode = 'keep' Preserve the data base file to enable restart + 'delete' Delete the data base file freeing all resources + + mode is overridden by opening the data base with + mode='scratch' in which instance it is always deleted + upon closing + + + int rtdb_get_info(const int handle, const char *name, int *ma_type, + int *nelem, char date[26]) + + Get info about an entry from the data base + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = returns MA type of the entry + nelem = returns no. of elements of the given type + date = returns date of insertion (null terminated character string) + + + int rtdb_put(const int handle, const char *name, const int ma_type, + const int nelem, const void *array) + + Insert an entry into the data base replacing previous entry + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = MA type of the entry + nelem = no. of elements of the given type + array = data to be inserted + + + int rtdb_get(const int handle, const char *name, const int ma_type, + const int nelem, void *array) + + Get an entry from the data base + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = MA type of the entry which must match entry type + nelem = size of array in units of ma_type + array = user provided buffer that returns data + + int rtdb_ma_get(const int handle, const char *name, int *ma_type, + int *nelem, int *ma_handle) + + Get an entry from the data base returning an MA handle + + handle = handle to RTDB + name = entry name (null terminated character string) + ma_type = returns MA type of the entry + nelem = returns no. of elements of type ma_type in data + ma_handle= returns MA handle to data + + int rtdb_first(const int handle, const int namelen, char *name) + + Return the name of the first (user inserted) entry in the data base. + The order is effectively random. + + handle = handle to RTDB + namelen = size of user provided buffer name + name = name of entry is returned in this buffer + + + int rtdb_next(const int handle, const int namelen, char *name) + + Return the name of the next (user inserted) entry in the data base. + The order is effectively random. + + handle = handle to RTDB + namelen = size of user provided buffer name + name = name of entry is returned in this buffer + + + int rtdb_print(const int handle, const int print_values) + + Print the contents of the data base to stdout + + handle = handle to RTDB + print_values = boolean flag ... if true values as well as + keys are printed out. + + + int rtdb_delete(const int handle, const char *name) + + Delete the entry from the database. + Return + 1 if key was present and successfully deleted + + 0 if key was not present, or if an error occured + + handle = handle to RTDB + name = name of entry to delete + +*/ + +#include + + bool rtdb_open(const char *, const char *, FILE *); + bool rtdb_close(FILE *, const char *); + bool rtdb_put(const int, const char *, const int, const int, const void *); + bool rtdb_get(const int, const char *, const int, const int, void *); + bool rtdb_get_info(const int, const char *, int *, int *, char [26]); + bool rtdb_ma_get(const int, const char *, int *, int *, int *); + bool rtdb_first(const int, const int, char *); + bool rtdb_next(const int, const int, char *); + bool rtdb_print(const int, const int); + bool rtdb_delete(const int, const char *); + +/* + Following are 'parallel' versions of the above where only + process 0 actually accesses the data base and all others + just get its output. +*/ + + bool rtdb_par_open(const char *, const char *, FILE *); + bool rtdb_par_close(FILE *, const char *); + bool rtdb_par_put(const int, const char *, const int, const int, const void *); + bool rtdb_par_get(const int, const char *, const int, const int, void *); + bool rtdb_par_get_info(const int, const char *, int *, int *, char [26]); + bool rtdb_par_ma_get(const int, const char *, int *, int *, int *); + bool rtdb_par_first(const int, const int, char *); + bool rtdb_par_next(const int, const int, char *); + bool rtdb_par_print(const int, const int); + bool rtdb_par_delete(const int, const char *); + +#endif // _RTDB_H From d4bd5d13bfc12193bd497d21b27e28284318722d Mon Sep 17 00:00:00 2001 From: Adam Parler Date: Sun, 21 Jan 2024 00:01:51 -0800 Subject: [PATCH 11/11] continued translation of files (mostly inp.c) --- src/config/makefile.h | 10 +- src/inp/GNUmakefile | 2 +- src/inp/inp.c | 630 +++++++++++++++++++++++++++++++++++++++++ src/inp/inp.h | 23 +- src/inp/inpP.h | 2 +- src/input/GNUmakefile | 8 + src/input/design | 18 ++ src/input/input.format | 179 ++++++++++++ src/util/itri.h | 13 + src/util/output.c | 290 +++++++++++++++++++ src/util/util.h | 6 + 11 files changed, 1159 insertions(+), 22 deletions(-) create mode 100644 src/inp/inp.c create mode 100644 src/input/GNUmakefile create mode 100644 src/input/design create mode 100644 src/input/input.format create mode 100644 src/util/itri.h create mode 100644 src/util/output.c create mode 100644 src/util/util.h diff --git a/src/config/makefile.h b/src/config/makefile.h index 1669144..522dd7b 100644 --- a/src/config/makefile.h +++ b/src/config/makefile.h @@ -161,15 +161,7 @@ ifeq ($(EXPLICITF),TRUE) # with CPP to get .f files # .SUFFIXES: -.SUFFIXES: .o .s .F .f .c - -.F.o: - $(MAKE) $*.f - $(FC) -c $(FFLAGS) $*.f - /bin/rm -f $*.f - -.F.f: - $(CPP) $(INCLUDES) $(DEFINES) < $*.F | sed '/^#/D' > $*.f +.SUFFIXES: .o .s .c .c.o: $(CC) $(CFLAGS) -c $*.c diff --git a/src/inp/GNUmakefile b/src/inp/GNUmakefile index 94c090a..17383c8 100644 --- a/src/inp/GNUmakefile +++ b/src/inp/GNUmakefile @@ -3,7 +3,7 @@ OBJ = inp.o LIBRARY = libinp.a LIB_TARGETS = test.o test - HEADERS = inp.fh + HEADERS = inp.h include ../config/makefile.h diff --git a/src/inp/inp.c b/src/inp/inp.c new file mode 100644 index 0000000..9cb1eb7 --- /dev/null +++ b/src/inp/inp.c @@ -0,0 +1,630 @@ +#include +#include + +#include "inpP.h" + +int iread = 5; +int iwrite = 6; +int jrec = -1; +int jump = 0; +bool oswit = false; +int nerr = 999; +int nline = 0; +int noline = 0; +int ierrpos = -1; +char errmsg[2] = " "; +int input_line = 0; +char xblnk[2] = " "; +char xtab[2] = "\t"; +char xsplit[2] = ";"; +char xcomm[2] = "#"; +char xback[2] = "\\"; +char xquote[2] = "\""; + + +void inp_init(int ir, int iw) { + iread = ir; + iwrite = iw; + jrec = -1; + jump = 0; + oswit = false; + nerr = 999; + nline = 0; + noline = 0; + ierrpos = -1; + errmsg[0] = ' '; + input_line = 0; +} + +int inp_n_field() { + + // return no. of fields in the input line ... 0 = EOF + return jump; +} + +int inp_cur_field() { + + // return no. of fields processed so far (0,...,inp_n_field()) + return jrec; +} + +void inp_set_field(int ivalue) { + + // set field to be read next (ivalue=0,...,inp_n_field()) + if (ivalue < 0 || ivalue > inp_n_field()) { + errquit('inp_set_field: stupid field value',ivalue); + } + jrec = ivalue; + + ierrpos = -1; + strcpy(errmsg, " "); + +} + +bool inp_line(char *z) { + + /* + set the variable z to be as much of the current input line + that it can hold + */ + + bool ret_val; + if (jump > 0) { + strcpy(z, ia); + ret_val = true; + ierrpos = -1; + strcpy(errmsg, " "); + } else { + strcpy(errmsg, "no input line available"); + ierrpos = -1; + ret_val = false; + } + + return ret_val; +} + +bool ois_ws(char xtest) { + return strcmp(xtest, xblnk) == 0 || strcmp(xtest, xtab) == 0; +} + +bool inp_read() { +/* + this routine reads a data card and scans it for non - space fields + the number of fields is stored in jump, the starting point of a + field in istrt(i) and the number of characters in that field + in inumb(i). +*/ + int ncol[MAX_FIELD], lenja, i, iwidth, j, jwidth, k, mark, nbegin, nfini; + bool ios_ws, ret_val; + char tmp[MAX_WIDTH], xprev; + + nline++; + if (nline <= noline) { + goto L150; + } + + if (oswit) { + ierrpos = -1; + strcpy(errmsg, "unexpected end of data file"); + jump = 0; + jrec = 0; + return false; + } else { + ierrpos = -1; + strcpy(errmsg, " "); + } + + // read next physical input line + lenja = 0; +L100: + scanf("%s", ja + lenja); + input_line++; + lenja = strlen(ja); + + // Check for . * eof at beginning of line to indicate EOF + if (lenja == 1 && (ja[0] == '.' || ja[0] == '*')) { + goto L300; + } + if (lenja == 3 && strcmp(ja, "eof") == 0) { + goto L300; + } + + // handle blank lines and concatenation using backslash + if (lenja == 0) { + goto L100; + } else { + if (ja[lenja - 1] == xback) { + ja[lenja - 1] = xblnk; + goto L100; + } + } + jwidth = strlen(ja); + + // handle comments from # to eol ... allow for backslash quoting + xprev = xblnk; + for (i = 0; i < jwidth; i++) { + if (ja[i] == xcomm && xprev != xback) { + lenja = strlen(ja); + printf("\n comment :- %s", ja + i + 1); + memset(ja + i, xblnk, MAX_WIDTH - i); + break; + } else if (ja[i] == xcomm && xprev == xback) { + strcpy(tmp, ja); + memmove(ja + i - 1, tmp + i, MAX_WIDTH - i); + xprev = xblnk; + continue; + } + strcpy(xprev, ja[i]); + } + + /* + figure out where ; splits physical line into multiple logical lines + again handling quoted backslash + */ + k = jwidth; + mark = 0; + xprev = xblnk; + for (i = 0; i < jwidth; i++) { + if (ja[i] == xsplit && xprev != xback) { + mark = mark + 1; + ncol[mark] = i; + } else if (ja[i] == xsplit && xprev == xback) { + strcpy(tmp, ja); + memmove(ja + i - 1, tmp + i, MAX_WIDTH - i); + xprev = xblnk; + continue; + } + xprev = ja[i]; + } + + noline = 1; + if (mark == 0) { + nstart[noline] = 1; + nend[noline] = jwidth; + } else { + i = ncol[mark] + 1; + if (i <= jwidth) { + for (j = i; j < jwidth; j++) { + if (!ois_ws(ja[j])) { + goto L170; + } + } + } + k = ncol[mark] - 1; + mark = mark - 1; +L170: + noline = mark + 1; + nstart[1] = 1; + for (i = 1; i <= mark; i++) { + j = ncol[i]; + nend[i] = j - 1; + nstart[i + 1] = j + 1; + } + nend[noline] = k; + } + nline = 1; + + // Start processing next logical input line (put into ia(1:iwidth)) +L150: + jump = 0; + jrec = 0; + nbegin = nstart[nline]; + nfini = nend[nline]; + iwidth = nfini - nbegin + 1; + memset(ia, xblnk, MAX_WIDTH); + memcpy(ia, ja + nbegin - 1, iwidth); + /* + partition input line into strings inside double quotes or + white space separated fields + */ + i = 1; +L151: + for (j = i; j <= iwidth; j++) { + if (!ois_ws(ia[j])) { + goto L152; + } + } + goto L155; +L152: + i = j; + jump++; + istrt[jump] = i; + if (ia[i] == xquote) { + for (j = i + 1; j <= iwidth; j++) { + if (ia[j] == xquote && ia[j - 1] != xback) { + break; + } else if (ia[j] == xquote && ia[j - 1] == xback) { + strcpy(tmp, ia); + memmove(ia + j - 1, tmp + j, MAX_WIDTH - j); + continue; + } + } + ierrpos = j; + strcpy(errmsg, "no terminating quote for string"); + return false; + } else { + for (j = i + 1; j <= iwidth; j++) { + if (ois_ws(ia[j])) { + break; + } + } + j--; + } + + inumb[jump] = j - istrt[jump] + 1; + i = j + 1; + goto L151; +L155: + if (jump > 0) { + iwidth = istrt[jump] + inumb[jump] - 1; + } + return true; +L300: + oswit = true; + ierrpos = -1; + strcpy(errmsg, "unexpected end of data file"); + jump = 0; + jrec = 0; + return false; +} + +bool inp_eof() { + return oswit; +} + +void inp_errout() { + char xpt, xstp; + xpt = '*'; + xstp = '.'; + int length, i; +/* + If an error has occured print out the error message + and the position in the current input line +*/ + if (strcmp(errmsg, " ") != 0) { + length = strlen(errmsg); + printf("input error at line %d: %s\n", input_line, errmsg); + jrec = -1; + printf("%s\n", ia); + if (ierrpos > 0) { + for (i = 0; i < ierrpos; i++) { + tmp[i] = xstp; + } + tmp[ierrpos] = xpt; + printf("%s\n", tmp); + } + } +} + +void inp_outrec() { + // Write out the current input line + printf("%s\n", ia); +} + +#include +#include + +bool inp_a(char* a) { +/* + Return field as character string, minus any enclosing quotes + with an error if it does not fit +*/ + int i1, i2, length; + bool ret_val; + + ierrpos = -1; + strcpy(errmsg, " "); + + if (jrec >= jump) { + a = xblnk; + ierrpos = 0; + strcpy(errmsg, "at end of line looking for character string"); + return false; + } + + i1 = istrt[jrec+1]; + i2 = istrt[jrec+1] + inumb[jrec+1] - 1; + + if (ia[i1] == xquote && ia[i2] == xquote) { + i1 = i1 + 1; + length = inumb[jrec+1] - 2; + } else { + length = inumb[jrec+1]; + } + + if (strlen(a) < length) { + a = xblnk; + ierrpos = 0; + strcpy(errmsg, "inp_a: string is too large for argument"); + return false; + } else { + jrec = jrec + 1; + strncpy(a, ia + i1, length); + return true; + } +} +logical function inp_a_trunc(a) + implicit none + + character*1 xblnk, xquote + character*(*) a +c +c Return field as character string, minus any enclosing quotes +c quietly truncating if it does not fit +c + ierrpos = -1 + errmsg = ' ' + if(jrec .ge. jump) then + a = xblnk + inp_a_trunc = .false. + ierrpos = 0 + errmsg = 'at end of line looking for character string' + return + endif + i1 = istrt(jrec+1) + i2 = istrt(jrec+1)+inumb(jrec+1)-1 + if (ia(i1:i1).eq.xquote .and. ia(i2:i2).eq.xquote) then + i1 = i1+1 + length = inumb(jrec+1)-2 + else + length = inumb(jrec+1) + endif + jrec = jrec + 1 + a = ia(i1:i1+length-1) + inp_a_trunc = .true. + return +c + end +logical function inp_f (buf) + implicit none + + double precision ten, buf + character*1 xchar(15) + data xchar /'0','1','2','3','4','5','6','7','8','9' + 1 ,'+','-','.','e','d'/ + data ten/10.0d0/ +c + ierrpos = -1 + errmsg = ' ' + buf=0.0d0 + if (jrec.ge.jump) then + inp_f = .false. + errmsg = 'at end of line looking for floating point number' + ierrpos=-1 + return + endif + jrec=jrec+1 + i1=istrt(jrec) + i2=i1+inumb(jrec)-1 + ie2=i2 +c... sign + isign=1 + if (ia(i1:i1).eq.xchar(12))isign=-1 + if (ia(i1:i1).eq.xchar(12).or.ia(i1:i1).eq.xchar(11)) i1=i1+1 +c... exponent + do ie=i1,i2 + if (ia(ie:ie).eq.xchar(14) .or. ia(ie:ie).eq.xchar(15)) goto 20 + enddo + iexp=0 + go to 50 + 20 i2=ie-1 + iexp=1 + ie1=ie+1 + if (ia(ie1:ie1).eq.xchar(12))iexp=-1 + if (ia(ie1:ie1).eq.xchar(12).or.ia(ie1:ie1).eq.xchar(11)) + * ie1=ie1+1 + ibuff=0 + do i=ie1,ie2 + do j=1,10 + if (ia(i:i).eq.xchar(j)) go to 41 + enddo + goto 100 + 41 ibuff=ibuff*10+j-1 + enddo + iexp=iexp*ibuff +c.... the number itself + 50 orep=.false. + do i=i1,i2 + if(ia(i:i).ne.xchar(13)) then + do j=1,10 + if (ia(i:i).eq.xchar(j)) go to 70 + enddo + goto 100 + 70 buf=buf*ten+ dfloat(j-1) + else + if(orep)go to 100 + iexp=iexp+i-i2 + orep=.true. + endif + enddo + buf = buf * dfloat(isign) * ten**iexp + inp_f = .true. + return +c + 100 inp_f = .false. + jrec = jrec-1 ! Position to re-read the field + ierrpos = i + errmsg = 'illegal character reading floating point number' +c + end +logical function inp_i(jbuf) + implicit none + + character*1 xchar(12) + integer jbuf + data xchar /'0','1','2','3','4','5','6','7','8','9' + 1 ,'+','-'/ +c +c subroutine for reading integers from the array ia, +c starting at ia(istrt(jrec)) and going on for inumb(jrec)) +c elements. plus signs are ignored, the answer is accumulated +c in jbuf +c + ierrpos = -1 + errmsg = ' ' + jbuf = 0 + if(jrec.ge.jump) then + inp_i = .false. + ierrpos = -1 + errmsg = 'at end of line looking for integer' + return + endif + jrec = jrec + 1 + n = inumb(jrec) + ifact = 1 + ist=istrt(jrec) + nstrt = ist + n - 1 + do i = 1,n + xtemp = ia(nstrt:nstrt) + do j=1,12 + if(xchar(j).eq.xtemp)go to 130 + enddo + goto 120 +c + 130 if(j.ge.11) then + if(nstrt.ne.ist)go to 120 + if(j.ge.12)jbuf=-jbuf + go to 160 + endif + jbuf=jbuf+(j-1)*ifact + ifact = ifact * 10 + nstrt=nstrt-1 + enddo + 160 continue + inp_i = .true. + return +c + 120 ierrpos = nstrt + errmsg = 'illegal character when reading integer' + inp_i = .false. + jrec = jrec-1 + return +c + end +logical function inp_compare(ocase, a, b) + implicit none + logical ocase + character*(*) a, b + integer la, lb, i + character*1 atest, btest + integer inp_strlen + external inp_strlen +c + inp_compare = .false. + la = inp_strlen(a) + lb = inp_strlen(b) + if (la .gt. lb) then + return + else if (ocase) then + inp_compare = a .eq. b(1:la) + return + else + do i = 1, la + atest = a(i:i) + btest = b(i:i) + call inp_lcase(atest) + call inp_lcase(btest) + if (atest.ne.btest) return + enddo + inp_compare = .true. + return + endif +c + end +logical function inp_match(nrec, ocase, test, array, ind) + implicit none + integer nrec, ind + logical ocase, inp_compare + character*(*) test, array(*) + integer i, l, inp_strlen + external inp_compare, inp_strlen +c + l = inp_strlen(test) + inp_match = .false. + ind = -1 +c + do i=1,nrec + if (inp_compare(ocase, test(1:l), array(i))) then + if (inp_match) then + inp_match = .false. ! Ambiguity + ind = 0 + return + else + inp_match = .true. ! First match + ind = i + endif + endif + enddo +c + end +subroutine inp_prev_field() + implicit none + +c + call inp_set_field(max(0,inp_cur_field()-1)) +c + end +integer function inp_strlen(a) + implicit none + + character*(*) a + integer i + integer len + logical ois_ws + intrinsic len + ois_ws(xtest) = (xtest.eq.xblnk .or. xtest.eq.xtab) +c + do i = len(a),1,-1 + if (.not. ois_ws(a(i:i))) goto 10 + enddo +c + 10 inp_strlen = i +c + end +subroutine inp_lcase(string) + implicit none + character*(*) string + intrinsic ichar, len + integer i, length, uca, ucz, lca, shift, test +c + uca = ichar('A') ! MUST be uppercase A + ucz = ichar('Z') ! MUST be uppercase Z + lca = ichar('a') ! MUST be lowercase a + shift = lca - uca + if (shift .eq. 0) + $ call errquit('inp_lcase: check case of program source', 0) +c + length = len(string) + do i = 1, length + test = ichar(string(i:i)) + if (test.ge.uca .and. test.le.ucz) + $ string(i:i) = char(test+shift) + enddo +c + end +logical function inp_search(ocase, z) + implicit none + character*(*) z + logical ocase + character*256 tmp + integer length + integer inp_strlen + logical inp_read, inp_a, inp_compare + external inp_read, inp_a, inp_compare, inp_strlen +c + length = inp_strlen(z) +c + 10 if (inp_read()) then + if (inp_a(tmp)) then + if (inp_compare(ocase, z(1:length), tmp)) then + call inp_prev_field() + inp_search = .true. + return + endif + endif + goto 10 + endif +c + inp_search = .false. +c + end \ No newline at end of file diff --git a/src/inp/inp.h b/src/inp/inp.h index d86cb78..ec1f638 100644 --- a/src/inp/inp.h +++ b/src/inp/inp.h @@ -1,18 +1,19 @@ #ifndef _INP_H #define _INP_H +#include + + bool inp_i(int); + bool inp_f(double); + bool inp_a(char *); + bool inp_read(); + bool inp_line(char *); + bool inp_match(int, bool, char *, char *[], int); + bool inp_search(bool, char*); + bool inp_compare(bool, char *, char *); + bool inp_eof(); + bool inp_a_trunc(char *); - int inp_i(); - float inp_f(); - char *inp_a(); int inp_n_field(); int inp_cur_field(); - int inp_match(); - int inp_read(); - int inp_search(); - int inp_compare(); - int inp_strlen(); - int inp_line(); - int inp_eof(); - int inp_a_trunc(); #endif \ No newline at end of file diff --git a/src/inp/inpP.h b/src/inp/inpP.h index 0ddece8..f1d8a52 100644 --- a/src/inp/inpP.h +++ b/src/inp/inpP.h @@ -7,7 +7,7 @@ #define MAX_WIDTH 256 // Maximum no. of characters in an input line #define MAX_FIELD MAX_WIDTH/2 + 1 // Maximum no. of fields in an input line - char ja[256]; // Input buffers ... MUST match max_width + char ja[256], ia[256]; // Input buffers ... MUST match max_width char tmp[256]; // Same size work space char errmsg[80]; // Error message char xcomm; // Comment character diff --git a/src/input/GNUmakefile b/src/input/GNUmakefile new file mode 100644 index 0000000..a67d17a --- /dev/null +++ b/src/input/GNUmakefile @@ -0,0 +1,8 @@ + + OBJ = input_parse.o input_mem_size.o memory_input.o input_set.o \ + input_start_opt.o input_title.o + LIBRARY = libinput.a + +include ../config/makefile.h +include ../config/makelib.h + diff --git a/src/input/design b/src/input/design new file mode 100644 index 0000000..ac7c3f7 --- /dev/null +++ b/src/input/design @@ -0,0 +1,18 @@ + + + separate routine input_mem_size() scans input for memory directive + + separate routine input_rtdb_name() scans input to infer the rtdb name + + top level recognizes simple directives and module names only + + inp_read() + while (input available) + + read name + + match name against known directives and call appropriate + modules to handle the input + + + diff --git a/src/input/input.format b/src/input/input.format new file mode 100644 index 0000000..f037a2b --- /dev/null +++ b/src/input/input.format @@ -0,0 +1,179 @@ + +1) All input is free format and is lower cased on input except for + file names and titles. + +2) Directive structure + +3) Most directives can appear in any order + +4) Sensible defaults + full error checking +--------------------- + + +--------------------------------------------------------------------- +Directives +---------- + + Syntax for definition of the directives + + () used to group entries (not actually present in the input) + || separate exclusive formats + [] enclose optional entries with a default value + <> enclose a type and a name of a value to be specified + A string is just a sequence of characters, enclosed in + quotes if there is white space + \ is used to concatenate lines + + The order of keyed optional entries should not matter + unless noted otherwise. + +--------------------------------------------------------------------- +The input must commence with either a START or a RESTART directive +which have the same syntax + +(RESTART || START) \ + [[PREFIX] = (-'.db' || 'calc')] \ + [DATABASE = .db] + + These directives determine if this is a restart or startup calculation + and provide definition of and + In a startup calculation any existing data base is destroyed. + + By default all filenames will be created by appending to a common + file prefix, which could include a path adjustment. This defaults + to either the data base name, stripped of a trailing '.db', or + failing that 'calc'. + + The data base path can be specified, or defaulted using the + file prefix. + + E.g. + + start + + Startup using all defaults ( = 'calc') and + = 'calc.db' + + restart water + + Restart calculation with = 'water' and + = 'water.db' + + restart prefix water + + Same as previous example + + restart /tmp/rjh/ch2 database /tmp/rjh/ch2small.db + + Restart calculation with = '/tmp/rjh/ch2' and + = '/tmp/rjh/ch2/ch2small.db' + + start database /disk2/mgo.db + + Startup calculation with = '/disk2/mgo' and + = '/disk2/mgo.db' + + start database /disk2/mgo_dumpfile + + Startup calculation with = 'calc' and + = '/disk2/mgo_dumpfile' + +--------------------------------------------------------------------- + +TITLE + + Enters the string into the data base entry 'title' + +--------------------------------------------------------------------- + +GEOMETRY [ = 'geometry'] [[UNITS] = 'au'] + + read until encounter END + + +END + + Enters atomic cartesian coordinates in either atomic units (units + = 'au') or angstroms (units = 'angstroms'). + + Geometries may be optionally named, however, the default name of + 'geometry' must usually be present for a calculation to proceed. + + The atomic tag serves to match against tags provided for basis + function centers. Also, the first 1 or 2 characters of the atomic + tag may interpreted to identify the element. + + e.g. + + geometry 'water at 90 degrees' angs + o 8 0.0 0.0 0.0 + h 1 1.0 0.0 0.0 + h 1 0.0 1.0 0.0 + end +--------------------------------------------------------------------- + +BASIS [ = 'mo basis set'>] LIBRARY + Read until END encountered + + LIBRARY + + or + + + read until next or END encountered + + +END + + If the basis directive is not provided in a startup calculation + then a default of 3-21g is adopted. + + Basis sets may also be named, with the default name of 'mo basis set' + being that required by modules that compute MOs. + + Many standard basis sets are available in a library. These may be + used for the whole molecule or just for individual atoms. + Basis functions defined within the basis set directive add to those + adopted on the directive line. + + e.g. + + basis library ccpvdz + + Just use the standard cpvdz basis set + + basis + h s + 0.01 100. + 0.8 7. + h p + 1.0 1.0 + end + + Defines a rather stupid basis set for the atomic center with tag h. + + basis library 3-21g + o d + 1.0 0.001 + si library "somebody's standard diffuse polarization functions" + end + + Adopts a 3-1g basis set which is augmented with a d function + on centers with tag o and a standard set of functions on centers + with tag si. + +--------------------------------------------------------------------- + +RHF + + + + +--------------------------------------------------------------------- + +The CALCULATION directive will eventually control what calculations +are performed and in what order, with high level control of input +and output to each module. Right now, since there is only RHF +energy, it does very little ... in fact it is not even implemented. + +--------------------------------------------------------------------- diff --git a/src/util/itri.h b/src/util/itri.h new file mode 100644 index 0000000..e4bf5e6 --- /dev/null +++ b/src/util/itri.h @@ -0,0 +1,13 @@ +#ifndef _ITRI_H +#define _ITRI_H + +/* +c simple statement function for evaluating index into lower +c triangular packed array ... indices do not have to be ordered +c +c This file must be include immediately before the first executable +c statement +*/ + itri[i][j] = (max(i,j)*(max(i,j)-3))/2 + i + j; + +#endif // _ITRI_H \ No newline at end of file diff --git a/src/util/output.c b/src/util/output.c new file mode 100644 index 0000000..cb0b747 --- /dev/null +++ b/src/util/output.c @@ -0,0 +1,290 @@ +#include + +void output(double *z, int rowlow, int rowhi, int collow, int colhi, + int rowdim, int coldim, int nctl) { + +/*...................................................................... +c output prints a real*8 matrix in formatted form with numbered rows +c and columns. the input is as follows; +c matrix(*,*).........matrix to be output +c rowlow..............row number at which output is to begin +c rowhi...............row number at which output is to end +c collow..............column number at which output is to begin +c colhi...............column number at which output is to end +c rowdim..............row dimension of matrix(*,*) +c coldim..............column dimension of matrix(*,*) +c nctl................carriage control flag; 1 for single space +c 2 for double space +c 3 for triple space +c the parameters that follow matrix are all of type integer*4. the +c program is set up to handle 5 columns/page with a 1p5d24.15 format for +c the columns. if a different number of columns is required, change +c formats 1000 and 2000, and initialize kcol with the new number of +c columns. +c author; nelson h.f. beebe, quantum theory project, university of +c florida, gainesville +c....................................................................... +C$Id$*/ + int begin, kcol, nctl, i, j, last, k; + double zero = 0.0; + char asa[3][8] = {" ", "00000000", "--------"}; + char ctl, blank = ' '; + + kcol = 8; + if (rowhi < rowlow || colhi < collow) { + printf(" zero matrix\n"); + return; + } + + last = (colhi < collow + kcol - 1) ? colhi : collow + kcol - 1; + for (begin = collow; begin <= colhi; begin += kcol) { + for (i = begin; i <= last; i++) { + printf("%d ", i); + } + printf("\n"); + for (k = rowlow; k <= rowhi; k++) { + for (i = begin; i <= last; i++) { + if (z[k * rowdim + i] != zero) { + printf("%d ", k); + for (i = begin; i <= last; i++) { + printf("%f ", z[k * rowdim + i]); + } + printf("\n"); + break; + } + } + } + last = (last + kcol < colhi) ? last + kcol : colhi; + } +} + + subroutine zoutput (z,rowlow,rowhi,collow,colhi,rowdim,coldim, + $ nctl) +c....................................................................... +c output prints a complex*16 matrix in formatted form with numbered rows +c and columns. the input is as follows; +c matrix(*,*).........matrix to be output +c rowlow..............row number at which output is to begin +c rowhi...............row number at which output is to end +c collow..............column number at which output is to begin +c colhi...............column number at which output is to end +c rowdim..............row dimension of matrix(*,*) +c coldim..............column dimension of matrix(*,*) +c nctl................carriage control flag; 1 for single space +c 2 for double space +c 3 for triple space +c the parameters that follow matrix are all of type integer*4. the +c program is set up to handle 5 columns/page with a 1p5d24.15 format for +c the columns. if a different number of columns is required, change +c formats 1000 and 2000, and initialize kcol with the new number of +c columns. +c author; nelson h.f. beebe, quantum theory project, university of +c florida, gainesville +c....................................................................... +C$Id$ + implicit none + integer rowlow,rowhi,collow,colhi,rowdim,coldim,begin,kcol + integer nctl, i, j, last, k + double complex z(rowdim,coldim), zero + character*8 asa(3), ctl, blank +* character*8 column +* data column/'column' / + data asa/' ','00000000' , + 1 '--------' /,blank/' '/ + data kcol/8/ + data zero/0.d00/ + do 11 i=rowlow,rowhi + do 10 j=collow,colhi + if (z(i,j).ne.zero) go to 15 + 10 continue + 11 continue + write (6,3000) + 3000 format (/' zero matrix'/) + go to 3 + 15 continue + ctl = blank + if ((nctl.le.3).and.(nctl.gt.0)) ctl = asa(nctl) + if (rowhi.lt.rowlow) go to 3 + if (colhi.lt.collow) go to 3 + last = min(colhi,collow+kcol-1) + do 2 begin = collow,colhi,kcol +* write (6,1000) (column,i,i = begin,last) + write (6,1000) (i,i = begin,last) + do 1 k = rowlow,rowhi + do 4 i=begin,last + if (z(k,i).ne.zero) go to 5 + 4 continue + go to 1 + 5 write (6,2000) ctl,k,(z(k,i), i = begin,last) + 1 continue + last = min(last+kcol,colhi) + 2 continue + 3 return +* kcol = 4 +* 1000 format (/1h ,16x,3(a6,i3,2x),(a6,i3)) +* 2000 format (a1,3hrow,i4,2x,4f17.11) +* kcol = 8 +* +* if U like having rows and columns labelled with row and col +* use these +* +* 1000 format (/1h ,11x,7(a3,i3,3x),(a3,i3)) +* 2000 format (a1,'row',i4,1x,8f9.4) +c + 1000 format (/1h ,8x,7(' ',i3,3x),(' ',i3)) + 2000 format (a1,i4,1x,1p,16d9.2) + end +c + subroutine doutput (z,rowlow,rowhi,collow,colhi,rowdim,coldim, + $ nctl) +c....................................................................... +c output prints a real*8 matrix in formatted form with numbered rows +c and columns. the input is as follows; +c matrix(*,*).........matrix to be output +c rowlow..............row number at which output is to begin +c rowhi...............row number at which output is to end +c collow..............column number at which output is to begin +c colhi...............column number at which output is to end +c rowdim..............row dimension of matrix(*,*) +c coldim..............column dimension of matrix(*,*) +c nctl................carriage control flag; 1 for single space +c 2 for double space +c 3 for triple space +c the parameters that follow matrix are all of type integer*4. the +c program is set up to handle 5 columns/page with a 1p5d24.15 format for +c the columns. if a different number of columns is required, change +c formats 1000 and 2000, and initialize kcol with the new number of +c columns. +c author; nelson h.f. beebe, quantum theory project, university of +c florida, gainesville +c....................................................................... +C$Id$ + implicit none + integer rowlow,rowhi,collow,colhi,rowdim,coldim,begin,kcol + integer nctl, i, j, last, k + double precision z(rowdim,coldim), zero + character*8 asa(3), ctl, blank +* character*8 column +* data column/'column' / + data asa/' ','00000000' , + 1 '--------' /,blank/' '/ + data kcol/8/ + data zero/0.d00/ + do 11 i=rowlow,rowhi + do 10 j=collow,colhi + if (z(i,j).ne.zero) go to 15 + 10 continue + 11 continue + write (6,3000) + 3000 format (/' zero matrix'/) + go to 3 + 15 continue + ctl = blank + if ((nctl.le.3).and.(nctl.gt.0)) ctl = asa(nctl) + if (rowhi.lt.rowlow) go to 3 + if (colhi.lt.collow) go to 3 + last = min(colhi,collow+kcol-1) + do 2 begin = collow,colhi,kcol +* write (6,1000) (column,i,i = begin,last) + write (6,1000) (i,i = begin,last) + do 1 k = rowlow,rowhi + do 4 i=begin,last + if (z(k,i).ne.zero) go to 5 + 4 continue + go to 1 + 5 write (6,2000) ctl,k,(z(k,i), i = begin,last) + 1 continue + last = min(last+kcol,colhi) + 2 continue + 3 return +* kcol = 4 +* 1000 format (/1h ,16x,3(a6,i3,2x),(a6,i3)) +* 2000 format (a1,3hrow,i4,2x,4f17.11) +* kcol = 8 +* +* if U like having rows and columns labelled with row and col +* use these +* +* 1000 format (/1h ,11x,7(a3,i3,3x),(a3,i3)) +* 2000 format (a1,'row',i4,1x,8f9.4) +c + 1000 format (/1h ,8x,7(' ',i3,3x),(' ',i3)) + 2000 format (a1,i4,1x,1p,8d9.2) + end +c + subroutine ioutput (z,rowlow,rowhi,collow,colhi,rowdim,coldim, + $ nctl) +c....................................................................... +c output prints a real*8 matrix in formatted form with numbered rows +c and columns. the input is as follows; +c matrix(*,*).........matrix to be output +c rowlow..............row number at which output is to begin +c rowhi...............row number at which output is to end +c collow..............column number at which output is to begin +c colhi...............column number at which output is to end +c rowdim..............row dimension of matrix(*,*) +c coldim..............column dimension of matrix(*,*) +c nctl................carriage control flag; 1 for single space +c 2 for double space +c 3 for triple space +c the parameters that follow matrix are all of type integer*4. the +c program is set up to handle 5 columns/page with a 1p5d24.15 format for +c the columns. if a different number of columns is required, change +c formats 1000 and 2000, and initialize kcol with the new number of +c columns. +c author; nelson h.f. beebe, quantum theory project, university of +c florida, gainesville +c....................................................................... +C$Id$ + implicit none + integer rowlow,rowhi,collow,colhi,rowdim,coldim,begin,kcol + integer nctl, i, j, last, k + integer z(rowdim,coldim), zero + character*8 asa(3), ctl, blank +* character*8 column +* data column/'column' / + data asa/' ','00000000' , + 1 '--------' /,blank/' '/ + data kcol/8/ + data zero/0/ + do 11 i=rowlow,rowhi + do 10 j=collow,colhi + if (z(i,j).ne.zero) go to 15 + 10 continue + 11 continue + write (6,3000) + 3000 format (/' zero matrix'/) + go to 3 + 15 continue + ctl = blank + if ((nctl.le.3).and.(nctl.gt.0)) ctl = asa(nctl) + if (rowhi.lt.rowlow) go to 3 + if (colhi.lt.collow) go to 3 + last = min(colhi,collow+kcol-1) + do 2 begin = collow,colhi,kcol +* write (6,1000) (column,i,i = begin,last) + write (6,1000) (i,i = begin,last) + do 1 k = rowlow,rowhi + do 4 i=begin,last + if (z(k,i).ne.zero) go to 5 + 4 continue + go to 1 + 5 write (6,2000) ctl,k,(z(k,i), i = begin,last) + 1 continue + last = min(last+kcol,colhi) + 2 continue + 3 return +* kcol = 4 +* 1000 format (/1h ,16x,3(a6,i3,2x),(a6,i3)) +* 2000 format (a1,3hrow,i4,2x,4f17.11) +* kcol = 8 +* +* if U like having rows and columns labelled with row and col +* use these +* +* 1000 format (/1h ,11x,7(a3,i3,3x),(a3,i3)) +* 2000 format (a1,'row',i4,1x,8f9.4) +c + 1000 format (/1h ,8x,7(' ',i3,3x),(' ',i3)) + 2000 format (a1,i4,1x,8i9) + end \ No newline at end of file diff --git a/src/util/util.h b/src/util/util.h new file mode 100644 index 0000000..50c45a0 --- /dev/null +++ b/src/util/util.h @@ -0,0 +1,6 @@ +#ifndef _UTIL_H +#define _UTIL_H + +double ddot(); + +#endif // _UTIL_H \ No newline at end of file