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.vscode
bin/
build/
include/
lib/
### C ###
# Prerequisites
*.d
# Compiled Object files
*.o
*.ko
*.elf
*.obj
*.slo
# Linker output
*.ilk
*.map
*.exp
# Precompiled Headers
*.gch
*.pch
# Libraries
*.dll
*.so
*.so.*
*.dylib
*.lib
*.a
*.la
*.lo
*.lai
# Executables
*.exe
*.out # output files
*.app
*.i*86
*.x86_64
*.hex
# Debug files
*.dSYM/
*.su
*.idb
*.pdb
# Kernel Module Compile Results
*.mod*
*.smod
*.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
.DS_Store
# 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
*.a
*.lo
*.o
*.so

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LICENSE
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an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
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:
<program> Copyright (C) <year> <name of author>
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
<https://www.gnu.org/licenses/>.
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
<https://www.gnu.org/licenses/why-not-lgpl.html>.

40
Makefile
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@ -1,40 +0,0 @@
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)

2
README.md
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@ -1,2 +0,0 @@
# nwchem_convert
Converting NWChem code from FORTRAN to C/C++

16
src/Makefile
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@ -1,16 +0,0 @@
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 $@

15
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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

38
src/basis/bas.h Normal file
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#ifndef _BAS_H
#define _BAS_H
#include <stdbool.h>
#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_

194
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#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

273
src/basis/bas_input.c Normal file
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#include <stdio.h>
#include <stdbool.h>
#include "rtdb.h"
#include "context.h"
#include "geom.h"
#include "bas.h"
#include "inp.h"
void bas_input(FILE *rtdb) {
/*
basis [<name>] [library <standard set>] [file <filename>] \
[spherical|cartesian] [segment] [print]
tag library <standard set> [file <filename>]
tag <shell type>
<exponent> <contraction coefficients>
...
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 [<name>] [library <standard set>] \\\n");
printf(" [file <filename>] [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 <standard set> [file <filename>]
c tag <contraction type>
c <exponent> <contraction coefficients>
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 <standard set> [file <filename>]\n");
printf(" tag <contraction type>\n");
printf(" <exponent> <contraction coefficients>\n");
printf(" ... \n");
printf(" end basis\n");
errquit("bas_input_body: format error in the input", 0);
}

14
src/basis/bas_staticP.h Normal file
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#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

39
src/basis/basdeclsP.h Normal file
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#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

1410
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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 = <bra_g(ish).bra_g(jsh) | ket_g(ksh).ket_g(lsh)>
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 = <bra_g(ish).bra_g(jsh) | ket_g(ksh)>
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 = <bra_g(ish)|ket_g(jsh)>
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 = <i_g(ish).j_g(jsh).k_g(ksh)>
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)
----------------------

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/* 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:<tag> 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:<basis name>:<basis component> ...
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
-
*/

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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
****

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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

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#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

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#!/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 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()
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")
#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("/","_")
#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 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, get_aux=get_aux)
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])
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)
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")

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#include <stdio.h>
void bas_dummmmmm() {
int i;
i = 0;
}
int bas_print_known(FILE *rtdb) {
return 0;
}

170
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#include "bas.h"
#include "rtdb.h"
#include "geom.h"
#include <stdio.h>
#include <stdbool.h>
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;
}

168
src/config/makefile.h Normal file
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@ -0,0 +1,168 @@
# $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 .c
.c.o:
$(CC) $(CFLAGS) -c $*.c
endif

59
src/config/makelib.h Normal file
View file

@ -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 *~ \#*\#

45
src/data/amber_q/ABE.frg
View file

@ -1,45 +0,0 @@
# 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

23
src/data/amber_q/BNZ.frg
View file

@ -1,23 +0,0 @@
# 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

28
src/data/amber_q/BTH.frg
View file

@ -1,28 +0,0 @@
# 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

129
src/data/amber_q/BTH.sgm
View file

@ -1,129 +0,0 @@
# 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

26
src/data/amber_q/BTO.frg
View file

@ -1,26 +0,0 @@
# 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

115
src/data/amber_q/BTO.sgm
View file

@ -1,115 +0,0 @@
# 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

30
src/data/amber_q/BUT.frg
View file

@ -1,30 +0,0 @@
# 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

145
src/data/amber_q/BUT.sgm
View file

@ -1,145 +0,0 @@
# 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

5
src/data/amber_q/CA.frg
View file

@ -1,5 +0,0 @@
# Fragment definition for Calcium cation
$CA
1 1 1 0
CA
1CA Ca 0 0 0 1 1 2.000000 0.000000

13
src/data/amber_q/CTR.frg
View file

@ -1,13 +0,0 @@
# 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

7
src/data/amber_q/Ca.sgm
View file

@ -1,7 +0,0 @@
# 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

92
src/data/amber_q/DTT.frg
View file

@ -1,92 +0,0 @@
# 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

24
src/data/amber_q/EAM.frg
View file

@ -1,24 +0,0 @@
# 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

339
src/data/amber_q/FUC.sgm
View file

@ -1,339 +0,0 @@
# 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 0.00000E+00
24 23 24 0 0
0.000000 0.00000E+00
25 23 25 0 0
0.000000 0.00000E+00
26 23 26 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 21 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 14 0 0
0.000000 0.00000E+00
8 5 4 6 0 0
0.000000 0.00000E+00
9 5 4 14 0 0
0.000000 0.00000E+00
10 6 4 14 0 0
0.000000 0.00000E+00
11 4 6 7 0 0
0.000000 0.00000E+00
12 4 6 8 0 0
0.000000 0.00000E+00
13 7 6 8 0 0
0.000000 0.00000E+00
14 6 8 9 0 0
0.000000 0.00000E+00
15 6 8 10 0 0
0.000000 0.00000E+00
16 9 8 10 0 0
0.000000 0.00000E+00
17 8 10 11 0 0
0.000000 0.00000E+00
18 8 10 12 0 0
0.000000 0.00000E+00
19 8 10 13 0 0
0.000000 0.00000E+00
20 11 10 12 0 0
0.000000 0.00000E+00
21 11 10 13 0 0
0.000000 0.00000E+00
22 12 10 13 0 0
0.000000 0.00000E+00
23 4 14 15 0 0
0.000000 0.00000E+00
24 4 14 16 0 0
0.000000 0.00000E+00
25 4 14 17 0 0
0.000000 0.00000E+00
26 15 14 16 0 0
0.000000 0.00000E+00
27 15 14 17 0 0
0.000000 0.00000E+00
28 16 14 17 0 0
0.000000 0.00000E+00
29 14 17 18 0 0
0.000000 0.00000E+00
30 14 17 19 0 0
0.000000 0.00000E+00
31 14 17 21 0 0
0.000000 0.00000E+00
32 18 17 19 0 0
0.000000 0.00000E+00
33 18 17 21 0 0
0.000000 0.00000E+00
34 19 17 21 0 0
0.000000 0.00000E+00
35 17 19 20 0 0
0.000000 0.00000E+00
36 3 21 17 0 0
0.000000 0.00000E+00
37 3 21 22 0 0
0.000000 0.00000E+00
38 3 21 23 0 0
0.000000 0.00000E+00
39 17 21 22 0 0
0.000000 0.00000E+00
40 17 21 23 0 0
0.000000 0.00000E+00
41 22 21 23 0 0
0.000000 0.00000E+00
42 21 23 24 0 0
0.000000 0.00000E+00
43 21 23 25 0 0
0.000000 0.00000E+00
44 21 23 26 0 0
0.000000 0.00000E+00
45 24 23 25 0 0
0.000000 0.00000E+00
46 24 23 26 0 0
0.000000 0.00000E+00
47 25 23 26 0 0
0.000000 0.00000E+00
1 2 1 3 21 0 0
0 0.000000 0.00000E+00
2 4 1 3 21 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 14 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 14 0 0
0 0.000000 0.00000E+00
9 1 3 21 17 0 0
0 0.000000 0.00000E+00
10 1 3 21 22 0 0
0 0.000000 0.00000E+00
11 1 3 21 23 0 0
0 0.000000 0.00000E+00
12 1 4 6 7 0 0
0 0.000000 0.00000E+00
13 1 4 6 8 0 0
0 0.000000 0.00000E+00
14 5 4 6 7 0 0
0 0.000000 0.00000E+00
15 5 4 6 8 0 0
0 0.000000 0.00000E+00
16 14 4 6 7 0 0
0 0.000000 0.00000E+00
17 14 4 6 8 0 0
0 0.000000 0.00000E+00
18 1 4 14 15 0 0
0 0.000000 0.00000E+00
19 1 4 14 16 0 0
0 0.000000 0.00000E+00
20 1 4 14 17 0 0
0 0.000000 0.00000E+00
21 5 4 14 15 0 0
0 0.000000 0.00000E+00
22 5 4 14 16 0 0
0 0.000000 0.00000E+00
23 5 4 14 17 0 0
0 0.000000 0.00000E+00
24 6 4 14 15 0 0
0 0.000000 0.00000E+00
25 6 4 14 16 0 0
0 0.000000 0.00000E+00
26 6 4 14 17 0 0
0 0.000000 0.00000E+00
27 4 6 8 9 0 0
0 0.000000 0.00000E+00
28 4 6 8 10 0 0
0 0.000000 0.00000E+00
29 7 6 8 9 0 0
0 0.000000 0.00000E+00
30 7 6 8 10 0 0
0 0.000000 0.00000E+00
31 6 8 10 11 0 0
0 0.000000 0.00000E+00
32 6 8 10 12 0 0
0 0.000000 0.00000E+00
33 6 8 10 13 0 0
0 0.000000 0.00000E+00
34 9 8 10 11 0 0
0 0.000000 0.00000E+00
35 9 8 10 12 0 0
0 0.000000 0.00000E+00
36 9 8 10 13 0 0
0 0.000000 0.00000E+00
37 4 14 17 18 0 0
0 0.000000 0.00000E+00
38 4 14 17 19 0 0
0 0.000000 0.00000E+00
39 4 14 17 21 0 0
0 0.000000 0.00000E+00
40 15 14 17 18 0 0
0 0.000000 0.00000E+00
41 15 14 17 19 0 0
0 0.000000 0.00000E+00
42 15 14 17 21 0 0
0 0.000000 0.00000E+00
43 16 14 17 18 0 0
0 0.000000 0.00000E+00
44 16 14 17 19 0 0
0 0.000000 0.00000E+00
45 16 14 17 21 0 0
0 0.000000 0.00000E+00
46 14 17 19 20 0 0
0 0.000000 0.00000E+00
47 18 17 19 20 0 0
0 0.000000 0.00000E+00
48 21 17 19 20 0 0
0 0.000000 0.00000E+00
49 14 17 21 3 0 0
0 0.000000 0.00000E+00
50 14 17 21 22 0 0
0 0.000000 0.00000E+00
51 14 17 21 23 0 0
0 0.000000 0.00000E+00
52 18 17 21 3 0 0
0 0.000000 0.00000E+00
53 18 17 21 22 0 0
0 0.000000 0.00000E+00
54 18 17 21 23 0 0
0 0.000000 0.00000E+00
55 19 17 21 3 0 0
0 0.000000 0.00000E+00
56 19 17 21 22 0 0
0 0.000000 0.00000E+00
57 19 17 21 23 0 0
0 0.000000 0.00000E+00
58 3 21 23 24 0 0
0 0.000000 0.00000E+00
59 3 21 23 25 0 0
0 0.000000 0.00000E+00
60 3 21 23 26 0 0
0 0.000000 0.00000E+00
61 17 21 23 24 0 0
0 0.000000 0.00000E+00
62 17 21 23 25 0 0
0 0.000000 0.00000E+00
63 17 21 23 26 0 0
0 0.000000 0.00000E+00
64 22 21 23 24 0 0
0 0.000000 0.00000E+00
65 22 21 23 25 0 0
0 0.000000 0.00000E+00
66 22 21 23 26 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

33
src/data/amber_q/G31.frg
View file

@ -1,33 +0,0 @@
# 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

33
src/data/amber_q/G61.frg
View file

@ -1,33 +0,0 @@
# 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

32
src/data/amber_q/G64.frg
View file

@ -1,32 +0,0 @@
# 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

49
src/data/amber_q/GA1.frg
View file

@ -1,49 +0,0 @@
# 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

47
src/data/amber_q/GA2.frg
View file

@ -1,47 +0,0 @@
# This is an automatically generated fragment file
#
$GA2
21 1 1 0
GA2
1 C1 AC 3 0 0 1 1 0.099978 0.000000
2 H1 H2 0 0 0 1 1 0.138270 0.000000
3 OR OS 0 0 0 1 1 -0.406195 0.000000
4 C2 CT 0 0 0 1 1 0.089663 0.000000
5 H2 H1 0 0 0 1 1 0.135805 0.000000
6 O2 OG 4 0 0 1 1 -0.238542 0.000000
7 C3 CT 0 0 0 1 1 0.033403 0.000000
8 H3 H1 0 0 0 1 1 0.187600 0.000000
9 O3 OH 0 0 0 1 1 -0.643404 0.000000
10 HO3 HO 0 0 0 1 1 0.440276 0.000000
11 C4 CT 0 0 0 1 1 0.068168 0.000000
12 H4 H1 0 0 0 1 1 0.135844 0.000000
13 O4 OH 0 0 0 1 1 -0.642604 0.000000
14 HO4 HO 0 0 0 1 1 0.411897 0.000000
15 C5 CT 0 0 0 1 1 0.012908 0.000000
16 H5 H1 0 0 0 1 1 0.129065 0.000000
17 C6 CT 0 0 0 1 1 0.269049 0.000000
182H6 H1 0 0 0 1 1 0.039234 0.000000
193H6 H1 0 0 0 1 1 0.039234 0.000000
20 O6 OH 0 0 0 1 1 -0.708152 0.000000
21 HO6 HO 0 0 0 1 1 0.408503 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
20 21

65
src/data/amber_q/GA3.frg
View file

@ -1,65 +0,0 @@
# 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

383
src/data/amber_q/GA3.sgm
View file

@ -1,383 +0,0 @@
# 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
OS -0.369500 0.000000
4 C2 0 0 0 1 1
CT 0.088495 0.000000
5 H2 0 0 0 1 1
H1 0.128159 0.000000
6 C3 0 0 0 1 1
CT -0.003142 0.000000
7 H3 0 0 0 1 1
H1 0.070396 0.000000
8 O3 4 0 0 1 1
OG -0.202001 0.000000
9 C4 0 0 0 1 1
CT 0.054364 0.000000
10 H4 0 0 0 1 1
H1 0.123615 0.000000
11 O4 5 0 0 1 1
OG -0.141163 0.000000
12 C5 0 0 0 1 1
CT 0.132859 0.000000
13 H5 0 0 0 1 1
H1 0.042566 0.000000
14 C6 0 0 0 1 1
CT 0.015802 0.000000
152H6 0 0 0 1 1
H1 0.084992 0.000000
163H6 0 0 0 1 1
H1 0.084992 0.000000
17 O6 0 0 0 1 1
OH -0.590914 0.000000
18 HO6 0 0 0 1 1
HO 0.367747 0.000000
19 N 0 0 0 1 1
N -0.492386 0.000000
20 HN 0 0 0 1 1
H 0.238725 0.000000
21 CA 0 0 0 1 1
CT 0.086698 0.000000
22 HA 0 0 0 1 1
H1 0.054254 0.000000
23 CB 0 0 0 1 1
CT -0.300000 0.000000
242HB 0 0 0 1 1
HC 0.100000 0.000000
253HB 0 0 0 1 1
HC 0.100000 0.000000
264HB 0 0 0 1 1
HC 0.100000 0.000000
27 C 0 1 0 1 1
C 0.586128 0.000000
28 OC 0 0 0 1 1
O2 -0.793064 0.000000
29 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 3 12 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 19 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 6 9 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 9 12 0 0
0.000000 0.00000E+00
14 12 13 0 0
0.000000 0.00000E+00
15 12 14 0 0
0.000000 0.00000E+00
16 14 15 0 0
0.000000 0.00000E+00
17 14 16 0 0
0.000000 0.00000E+00
18 14 17 0 0
0.000000 0.00000E+00
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0.000000 0.00000E+00
20 19 20 0 0
0.000000 0.00000E+00
21 19 21 0 0
0.000000 0.00000E+00
22 21 22 0 0
0.000000 0.00000E+00
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0.000000 0.00000E+00
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0.000000 0.00000E+00
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0.000000 0.00000E+00
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28 27 28 0 0
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3 3 1 4 0 0
0.000000 0.00000E+00
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0.000000 0.00000E+00
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0.000000 0.00000E+00
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0.000000 0.00000E+00
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33 15 14 17 0 0
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34 16 14 17 0 0
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35 14 17 18 0 0
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36 4 19 20 0 0
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11 1 3 12 14 0 0
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25 6 4 19 20 0 0
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37 6 9 12 13 0 0
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39 10 9 12 3 0 0
0 0.000000 0.00000E+00
40 10 9 12 13 0 0
0 0.000000 0.00000E+00
41 10 9 12 14 0 0
0 0.000000 0.00000E+00
42 11 9 12 3 0 0
0 0.000000 0.00000E+00
43 11 9 12 13 0 0
0 0.000000 0.00000E+00
44 11 9 12 14 0 0
0 0.000000 0.00000E+00
45 3 12 14 15 0 0
0 0.000000 0.00000E+00
46 3 12 14 16 0 0
0 0.000000 0.00000E+00
47 3 12 14 17 0 0
0 0.000000 0.00000E+00
48 9 12 14 15 0 0
0 0.000000 0.00000E+00
49 9 12 14 16 0 0
0 0.000000 0.00000E+00
50 9 12 14 17 0 0
0 0.000000 0.00000E+00
51 13 12 14 15 0 0
0 0.000000 0.00000E+00
52 13 12 14 16 0 0
0 0.000000 0.00000E+00
53 13 12 14 17 0 0
0 0.000000 0.00000E+00
54 12 14 17 18 0 0
0 0.000000 0.00000E+00
55 15 14 17 18 0 0
0 0.000000 0.00000E+00
56 16 14 17 18 0 0
0 0.000000 0.00000E+00
57 4 19 21 22 0 0
0 0.000000 0.00000E+00
58 4 19 21 23 0 0
0 0.000000 0.00000E+00
59 4 19 21 27 0 0
0 0.000000 0.00000E+00
60 20 19 21 22 0 0
0 0.000000 0.00000E+00
61 20 19 21 23 0 0
0 0.000000 0.00000E+00
62 20 19 21 27 0 0
0 0.000000 0.00000E+00
63 19 21 23 24 0 0
0 0.000000 0.00000E+00
64 19 21 23 25 0 0
0 0.000000 0.00000E+00
65 19 21 23 26 0 0
0 0.000000 0.00000E+00
66 22 21 23 24 0 0
0 0.000000 0.00000E+00
67 22 21 23 25 0 0
0 0.000000 0.00000E+00
68 22 21 23 26 0 0
0 0.000000 0.00000E+00
69 27 21 23 24 0 0
0 0.000000 0.00000E+00
70 27 21 23 25 0 0
0 0.000000 0.00000E+00
71 27 21 23 26 0 0
0 0.000000 0.00000E+00
72 19 21 27 28 0 0
0 0.000000 0.00000E+00
73 19 21 27 29 0 0
0 0.000000 0.00000E+00
74 22 21 27 28 0 0
0 0.000000 0.00000E+00
75 22 21 27 29 0 0
0 0.000000 0.00000E+00
76 23 21 27 28 0 0
0 0.000000 0.00000E+00
77 23 21 27 29 0 0
0 0.000000 0.00000E+00
1 21 28 27 29 0 0
0 0.000000 0.00000E+00

47
src/data/amber_q/GAL.frg
View file

@ -1,47 +0,0 @@
# This is an automatically generated fragment file
#
$GAL
21 1 1 0
GAL
1 C1 AC 3 0 0 1 1 -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

45
src/data/amber_q/GAO.frg
View file

@ -1,45 +0,0 @@
# 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

45
src/data/amber_q/GC1.frg
View file

@ -1,45 +0,0 @@
# 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

41
src/data/amber_q/GC2.frg
View file

@ -1,41 +0,0 @@
# 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

229
src/data/amber_q/GC2.sgm
View file

@ -1,229 +0,0 @@
# This is an automatically generated segment file
#
4.600000
18 18 32 44 0 0 1 1
0.000000
1 C1 3 0 0 1 1
AC 0.230198 0.000000
2 H1 0 0 0 1 1
H2 0.144196 0.000000
3 OR 0 0 0 1 1
OS -0.353085 0.000000
4 C5 0 0 0 1 1
CT -0.295341 0.000000
5 H5 0 0 0 1 1
H1 0.274167 0.000000
6 C6 0 0 0 1 1
CT 0.072517 0.000000
72H6 0 0 0 1 1
H1 0.085401 0.000000
83H6 0 0 0 1 1
H1 0.085401 0.000000
9 O6 4 0 0 1 1
OG -0.234560 0.000000
10 C4 5 0 0 1 1
CT 0.239914 0.000000
11 H4 0 0 0 1 1
H1 0.212404 0.000000
12 C3 0 0 0 1 1
CT -0.128330 0.000000
13 H3 0 0 0 1 1
H1 0.011847 0.000000
14 O3 6 0 0 1 1
OS -0.142412 0.000000
15 C2 0 0 0 1 1
CT -0.038942 0.000000
16 H2 0 0 0 1 1
H1 0.160070 0.000000
17 N2 7 1 0 1 1
N -0.708636 0.000000
18 HN 0 0 0 1 1
H 0.385191 0.000000
1 1 2 0 0
0.000000 0.00000E+00
2 1 3 0 0
0.000000 0.00000E+00
3 1 15 0 0
0.000000 0.00000E+00
4 3 4 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 10 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 6 9 0 0
0.000000 0.00000E+00
11 10 11 0 0
0.000000 0.00000E+00
12 10 12 0 0
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15 12 15 0 0
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16 15 16 0 0
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17 15 17 0 0
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18 17 18 0 0
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1 2 1 3 0 0
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3 3 1 15 0 0
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4 1 3 4 0 0
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5 3 4 5 0 0
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6 3 4 6 0 0
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7 3 4 10 0 0
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8 5 4 6 0 0
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9 5 4 10 0 0
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12 4 6 8 0 0
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22 10 12 15 0 0
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23 13 12 14 0 0
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24 13 12 15 0 0
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25 14 12 15 0 0
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26 1 15 12 0 0
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27 1 15 16 0 0
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28 1 15 17 0 0
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29 12 15 16 0 0
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30 12 15 17 0 0
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31 16 15 17 0 0
0.000000 0.00000E+00
32 15 17 18 0 0
0.000000 0.00000E+00
1 2 1 3 4 0 0
0 0.000000 0.00000E+00
2 15 1 3 4 0 0
0 0.000000 0.00000E+00
3 2 1 15 12 0 0
0 0.000000 0.00000E+00
4 2 1 15 16 0 0
0 0.000000 0.00000E+00
5 2 1 15 17 0 0
0 0.000000 0.00000E+00
6 3 1 15 12 0 0
0 0.000000 0.00000E+00
7 3 1 15 16 0 0
0 0.000000 0.00000E+00
8 3 1 15 17 0 0
0 0.000000 0.00000E+00
9 1 3 4 5 0 0
0 0.000000 0.00000E+00
10 1 3 4 6 0 0
0 0.000000 0.00000E+00
11 1 3 4 10 0 0
0 0.000000 0.00000E+00
12 3 4 6 7 0 0
0 0.000000 0.00000E+00
13 3 4 6 8 0 0
0 0.000000 0.00000E+00
14 3 4 6 9 0 0
0 0.000000 0.00000E+00
15 5 4 6 7 0 0
0 0.000000 0.00000E+00
16 5 4 6 8 0 0
0 0.000000 0.00000E+00
17 5 4 6 9 0 0
0 0.000000 0.00000E+00
18 10 4 6 7 0 0
0 0.000000 0.00000E+00
19 10 4 6 8 0 0
0 0.000000 0.00000E+00
20 10 4 6 9 0 0
0 0.000000 0.00000E+00
21 3 4 10 11 0 0
0 0.000000 0.00000E+00
22 3 4 10 12 0 0
0 0.000000 0.00000E+00
23 5 4 10 11 0 0
0 0.000000 0.00000E+00
24 5 4 10 12 0 0
0 0.000000 0.00000E+00
25 6 4 10 11 0 0
0 0.000000 0.00000E+00
26 6 4 10 12 0 0
0 0.000000 0.00000E+00
27 4 10 12 13 0 0
0 0.000000 0.00000E+00
28 4 10 12 14 0 0
0 0.000000 0.00000E+00
29 4 10 12 15 0 0
0 0.000000 0.00000E+00
30 11 10 12 13 0 0
0 0.000000 0.00000E+00
31 11 10 12 14 0 0
0 0.000000 0.00000E+00
32 11 10 12 15 0 0
0 0.000000 0.00000E+00
33 10 12 15 1 0 0
0 0.000000 0.00000E+00
34 10 12 15 16 0 0
0 0.000000 0.00000E+00
35 10 12 15 17 0 0
0 0.000000 0.00000E+00
36 13 12 15 1 0 0
0 0.000000 0.00000E+00
37 13 12 15 16 0 0
0 0.000000 0.00000E+00
38 13 12 15 17 0 0
0 0.000000 0.00000E+00
39 14 12 15 1 0 0
0 0.000000 0.00000E+00
40 14 12 15 16 0 0
0 0.000000 0.00000E+00
41 14 12 15 17 0 0
0 0.000000 0.00000E+00
42 1 15 17 18 0 0
0 0.000000 0.00000E+00
43 12 15 17 18 0 0
0 0.000000 0.00000E+00
44 16 15 17 18 0 0
0 0.000000 0.00000E+00

275
src/data/amber_q/GC3.sgm
View file

@ -1,275 +0,0 @@
# This is an automatically generated segment file
#
4.600000
21 21 37 56 0 0 1 1
0.000000
1 OR 0 0 0 1 1
OS -0.353085 0.000000
2 C1 3 0 0 1 1
AC 0.230198 0.000000
3 H1 0 0 0 1 1
H2 0.216303 0.000000
4 C2 0 0 0 1 1
CT -0.038942 0.000000
5 H2 0 0 0 1 1
H1 0.160070 0.000000
6 N2 4 1 0 1 1
N -0.708636 0.000000
7 HN 0 0 0 1 1
H 0.385191 0.000000
8 C3 0 0 0 1 1
CT -0.128330 0.000000
9 H3 0 0 0 1 1
H1 0.011847 0.000000
10 O3 0 0 0 1 1
OH -0.142412 0.000000
11 HO3 0 0 0 1 1
HO 0.128828 0.000000
12 C4 0 0 0 1 1
CT 0.239914 0.000000
13 H4 0 0 0 1 1
H1 0.212404 0.000000
14 O4 0 0 0 1 1
OH -0.650871 0.000000
15 HO4 0 0 0 1 1
HO 0.449936 0.000000
16 C5 0 0 0 1 1
CT -0.295341 0.000000
17 H5 0 0 0 1 1
H1 0.274167 0.000000
18 C6 0 0 0 1 1
CT 0.072517 0.000000
192H6 0 0 0 1 1
H1 0.085401 0.000000
203H6 0 0 0 1 1
H1 0.085401 0.000000
21 O6 5 0 0 1 1
OS -0.234560 0.000000
1 1 2 0 0
0.000000 0.00000E+00
2 1 16 0 0
0.000000 0.00000E+00
3 2 3 0 0
0.000000 0.00000E+00
4 2 4 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 16 0 0
0.000000 0.00000E+00
2 1 2 3 0 0
0.000000 0.00000E+00
3 1 2 4 0 0
0.000000 0.00000E+00
4 3 2 4 0 0
0.000000 0.00000E+00
5 2 4 5 0 0
0.000000 0.00000E+00
6 2 4 6 0 0
0.000000 0.00000E+00
7 2 4 8 0 0
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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
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14 4 8 12 0 0
0.000000 0.00000E+00
15 9 8 10 0 0
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16 9 8 12 0 0
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17 10 8 12 0 0
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18 8 10 11 0 0
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19 8 12 13 0 0
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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
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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
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26 1 16 12 0 0
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27 1 16 17 0 0
0.000000 0.00000E+00
28 1 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 16 1 2 3 0 0
0 0.000000 0.00000E+00
2 16 1 2 4 0 0
0 0.000000 0.00000E+00
3 2 1 16 12 0 0
0 0.000000 0.00000E+00
4 2 1 16 17 0 0
0 0.000000 0.00000E+00
5 2 1 16 18 0 0
0 0.000000 0.00000E+00
6 1 2 4 5 0 0
0 0.000000 0.00000E+00
7 1 2 4 6 0 0
0 0.000000 0.00000E+00
8 1 2 4 8 0 0
0 0.000000 0.00000E+00
9 3 2 4 5 0 0
0 0.000000 0.00000E+00
10 3 2 4 6 0 0
0 0.000000 0.00000E+00
11 3 2 4 8 0 0
0 0.000000 0.00000E+00
12 2 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 2 4 8 9 0 0
0 0.000000 0.00000E+00
16 2 4 8 10 0 0
0 0.000000 0.00000E+00
17 2 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 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

61
src/data/amber_q/GCN.frg
View file

@ -1,61 +0,0 @@
# 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

95
src/data/amber_q/GDP.frg
View file

@ -1,95 +0,0 @@
# 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

45
src/data/amber_q/GL1.frg
View file

@ -1,45 +0,0 @@
# 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

45
src/data/amber_q/GL2.frg
View file

@ -1,45 +0,0 @@
# 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

49
src/data/amber_q/GL3.frg
View file

@ -1,49 +0,0 @@
# 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

49
src/data/amber_q/GL4.frg
View file

@ -1,49 +0,0 @@
# 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

275
src/data/amber_q/GL4.sgm
View file

@ -1,275 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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0.000000
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8 C3 0 0 0 1 1
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51
src/data/amber_q/GL5.frg
View file

@ -1,51 +0,0 @@
# 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

287
src/data/amber_q/GL5.sgm
View file

@ -1,287 +0,0 @@
# 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
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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
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6 O2 0 0 0 1 1
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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
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CT 0.142201 0.000000
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HO 0.444588 0.000000
16 C5 0 0 0 1 1
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49
src/data/amber_q/GL6.frg
View file

@ -1,49 +0,0 @@
# 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

275
src/data/amber_q/GL6.sgm
View file

@ -1,275 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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0.000000
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5 H2 0 0 0 1 1
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src/data/amber_q/GL7.frg
View file

@ -1,51 +0,0 @@
# This is an automatically generated fragment file
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#
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287
src/data/amber_q/GL7.sgm
View file

@ -1,287 +0,0 @@
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263
src/data/amber_q/GL8.sgm
View file

@ -1,263 +0,0 @@
# This is an automatically generated segment file
#
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287
src/data/amber_q/GLT.sgm
View file

@ -1,287 +0,0 @@
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H2 0.093541 0.000000
3 OR 0 0 0 1 1
OS -0.398138 0.000000
4 C2 0 0 0 1 1
CT -0.217512 0.000000
5 H2 0 0 0 1 1
H1 0.313003 0.000000
6 O2 0 0 0 1 1
OH -0.600540 0.000000
7 HO2 0 0 0 1 1
HO 0.351411 0.000000
8 C3 0 0 0 1 1
CT 0.163078 0.000000
9 H3 0 0 0 1 1
H1 0.175157 0.000000
10 O3 0 0 0 1 1
OH -0.674837 0.000000
11 HO3 0 0 0 1 1
HO 0.445163 0.000000
12 C4 0 0 0 1 1
CT 0.021437 0.000000
13 H4 0 0 0 1 1
H1 0.121208 0.000000
14 O4 0 0 0 1 1
OH -0.643926 0.000000
15 HO4 0 0 0 1 1
HO 0.426869 0.000000
16 C5 0 0 0 1 1
CT 0.315425 0.000000
17 H5 0 0 0 1 1
H1 0.169464 0.000000
18 C6 0 0 0 1 1
CT -0.351786 0.000000
192H6 0 0 0 1 1
H1 0.175893 0.000000
203H6 0 0 0 1 1
H1 0.175893 0.000000
21 O6 0 0 0 1 1
OH -0.577008 0.000000
22 HO6 0 0 0 1 1
HO 0.423943 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
22 21 22 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
38 18 21 22 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
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18 5 4 8 9 0 0
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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
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35 10 8 12 16 0 0
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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
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

105
src/data/amber_q/GNP.frg
View file

@ -1,105 +0,0 @@
# 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

401
src/data/amber_q/GTL.sgm
View file

@ -1,401 +0,0 @@
# 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
7 5 7 0 0
0.000000 0.00000E+00
8 5 20 0 0
0.000000 0.00000E+00
9 7 8 0 0
0.000000 0.00000E+00
10 7 9 0 0
0.000000 0.00000E+00
11 7 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 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
0.000000 0.00000E+00
19 15 18 0 0
0.000000 0.00000E+00
20 18 19 0 0
0.000000 0.00000E+00
21 20 21 0 0
0.000000 0.00000E+00
22 20 22 0 0
0.000000 0.00000E+00
23 22 23 0 0
0.000000 0.00000E+00
24 22 24 0 0
0.000000 0.00000E+00
25 22 28 0 0
0.000000 0.00000E+00
26 24 25 0 0
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27 24 26 0 0
0.000000 0.00000E+00
28 24 27 0 0
0.000000 0.00000E+00
29 28 29 0 0
0.000000 0.00000E+00
30 28 30 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
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0.000000 0.00000E+00
8 1 5 6 0 0
0.000000 0.00000E+00
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10 1 5 20 0 0
0.000000 0.00000E+00
11 6 5 7 0 0
0.000000 0.00000E+00
12 6 5 20 0 0
0.000000 0.00000E+00
13 7 5 20 0 0
0.000000 0.00000E+00
14 5 7 8 0 0
0.000000 0.00000E+00
15 5 7 9 0 0
0.000000 0.00000E+00
16 5 7 10 0 0
0.000000 0.00000E+00
17 8 7 9 0 0
0.000000 0.00000E+00
18 8 7 10 0 0
0.000000 0.00000E+00
19 9 7 10 0 0
0.000000 0.00000E+00
20 7 10 11 0 0
0.000000 0.00000E+00
21 7 10 12 0 0
0.000000 0.00000E+00
22 7 10 13 0 0
0.000000 0.00000E+00
23 11 10 12 0 0
0.000000 0.00000E+00
24 11 10 13 0 0
0.000000 0.00000E+00
25 12 10 13 0 0
0.000000 0.00000E+00
26 4 13 10 0 0
0.000000 0.00000E+00
27 4 13 14 0 0
0.000000 0.00000E+00
28 4 13 15 0 0
0.000000 0.00000E+00
29 10 13 14 0 0
0.000000 0.00000E+00
30 10 13 15 0 0
0.000000 0.00000E+00
31 14 13 15 0 0
0.000000 0.00000E+00
32 13 15 16 0 0
0.000000 0.00000E+00
33 13 15 17 0 0
0.000000 0.00000E+00
34 13 15 18 0 0
0.000000 0.00000E+00
35 16 15 17 0 0
0.000000 0.00000E+00
36 16 15 18 0 0
0.000000 0.00000E+00
37 17 15 18 0 0
0.000000 0.00000E+00
38 15 18 19 0 0
0.000000 0.00000E+00
39 5 20 21 0 0
0.000000 0.00000E+00
40 5 20 22 0 0
0.000000 0.00000E+00
41 21 20 22 0 0
0.000000 0.00000E+00
42 20 22 23 0 0
0.000000 0.00000E+00
43 20 22 24 0 0
0.000000 0.00000E+00
44 20 22 28 0 0
0.000000 0.00000E+00
45 23 22 24 0 0
0.000000 0.00000E+00
46 23 22 28 0 0
0.000000 0.00000E+00
47 24 22 28 0 0
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48 22 24 25 0 0
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49 22 24 26 0 0
0.000000 0.00000E+00
50 22 24 27 0 0
0.000000 0.00000E+00
51 25 24 26 0 0
0.000000 0.00000E+00
52 25 24 27 0 0
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53 26 24 27 0 0
0.000000 0.00000E+00
54 22 28 29 0 0
0.000000 0.00000E+00
55 22 28 30 0 0
0.000000 0.00000E+00
56 29 28 30 0 0
0.000000 0.00000E+00
1 2 1 4 13 0 0
0 0.000000 0.00000E+00
2 3 1 4 13 0 0
0 0.000000 0.00000E+00
3 5 1 4 13 0 0
0 0.000000 0.00000E+00
4 2 1 5 6 0 0
0 0.000000 0.00000E+00
5 2 1 5 7 0 0
0 0.000000 0.00000E+00
6 2 1 5 20 0 0
0 0.000000 0.00000E+00
7 3 1 5 6 0 0
0 0.000000 0.00000E+00
8 3 1 5 7 0 0
0 0.000000 0.00000E+00
9 3 1 5 20 0 0
0 0.000000 0.00000E+00
10 4 1 5 6 0 0
0 0.000000 0.00000E+00
11 4 1 5 7 0 0
0 0.000000 0.00000E+00
12 4 1 5 20 0 0
0 0.000000 0.00000E+00
13 1 4 13 10 0 0
0 0.000000 0.00000E+00
14 1 4 13 14 0 0
0 0.000000 0.00000E+00
15 1 4 13 15 0 0
0 0.000000 0.00000E+00
16 1 5 7 8 0 0
0 0.000000 0.00000E+00
17 1 5 7 9 0 0
0 0.000000 0.00000E+00
18 1 5 7 10 0 0
0 0.000000 0.00000E+00
19 6 5 7 8 0 0
0 0.000000 0.00000E+00
20 6 5 7 9 0 0
0 0.000000 0.00000E+00
21 6 5 7 10 0 0
0 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
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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
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43 11 10 13 4 0 0
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44 11 10 13 14 0 0
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45 11 10 13 15 0 0
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46 12 10 13 4 0 0
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48 12 10 13 15 0 0
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49 4 13 15 16 0 0
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50 4 13 15 17 0 0
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51 4 13 15 18 0 0
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52 10 13 15 16 0 0
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53 10 13 15 17 0 0
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54 10 13 15 18 0 0
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55 14 13 15 16 0 0
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56 14 13 15 17 0 0
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57 14 13 15 18 0 0
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58 13 15 18 19 0 0
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59 16 15 18 19 0 0
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60 17 15 18 19 0 0
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61 5 20 22 23 0 0
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62 5 20 22 24 0 0
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63 5 20 22 28 0 0
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64 21 20 22 23 0 0
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65 21 20 22 24 0 0
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66 21 20 22 28 0 0
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67 20 22 24 25 0 0
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68 20 22 24 26 0 0
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69 20 22 24 27 0 0
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70 23 22 24 25 0 0
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71 23 22 24 26 0 0
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72 23 22 24 27 0 0
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73 28 22 24 25 0 0
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74 28 22 24 26 0 0
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75 28 22 24 27 0 0
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76 20 22 28 29 0 0
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77 20 22 28 30 0 0
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78 23 22 28 29 0 0
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79 23 22 28 30 0 0
0 0.000000 0.00000E+00
80 24 22 28 29 0 0
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81 24 22 28 30 0 0
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1 22 29 28 30 0 0
0 0.000000 0.00000E+00

103
src/data/amber_q/GTP.frg
View file

@ -1,103 +0,0 @@
# 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

34
src/data/amber_q/HDH.frg
View file

@ -1,34 +0,0 @@
# 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

169
src/data/amber_q/HDH.sgm
View file

@ -1,169 +0,0 @@
# 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
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O -0.502975 0.000000
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53H2 0 0 0 1 1
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6 C3 0 0 0 1 1
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7 H3 0 0 0 1 1
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8 O3 0 0 0 1 1
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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
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13 C5 4 0 0 1 1
CT -0.100000 0.000000
142H5 0 0 0 1 1
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153H5 0 0 0 1 1
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32
src/data/amber_q/HDO.frg
View file

@ -1,32 +0,0 @@
# This is an automatically generated fragment file
#
$HDO
14 1 1 0
HDO
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

157
src/data/amber_q/HDO.sgm
View file

@ -1,157 +0,0 @@
# 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 -0.180797 0.000000
42H2 0 0 0 1 1
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53H2 0 0 0 1 1
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6 C3 0 0 0 1 1
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7 H3 0 0 0 1 1
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8 O3 4 0 0 1 1
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12 C5 5 0 0 1 1
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161
src/data/amber_q/HED.sgm
View file

@ -1,161 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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44HZ 0 0 0 1 1
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5 C1 0 0 0 1 1
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156
src/data/amber_q/HEM.frg
View file

@ -1,156 +0,0 @@
$HEM
73 1 1 0
HEM
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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
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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
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37 HHC HC 0 0 0 1 1 0.130000 0.000000
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40 C2C CB 0 4 0 1 1 -0.280000 0.000000
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433HMC HC 0 0 0 1 1 0.100000 0.000000
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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
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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
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673HAD HC 0 0 0 1 1 0.100000 0.000000
68 CBD CT 0 0 0 1 1 -0.200000 0.000000
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703HBD HC 0 0 0 1 1 0.100000 0.000000
71 CGD C 0 1 0 1 1 0.350000 0.000000
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1 2
1 23
1 39
1 55
2 3
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50
src/data/amber_q/HEP.frg
View file

@ -1,50 +0,0 @@
# This is an automatically generated fragment file
# Atom types and connectivity were derived from coordinates
# Atomic partial charges are crude guestimations
#
$HEP
22 1 1 0
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271
src/data/amber_q/HEP.sgm
View file

@ -1,271 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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51
src/data/amber_q/HP1.frg
View file

@ -1,51 +0,0 @@
# This is an automatically generated fragment file
#
$HP1
23 1 1 0
HP1
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2 H1 H2 0 0 0 1 1 0.241979 0.000000
3 OR OS 0 0 0 1 1 -0.415373 0.000000
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7 HO2 HO 0 0 0 1 1 0.482404 0.000000
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203H7 H1 0 0 0 1 1 0.132550 0.000000
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1 3
1 4
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4 5
4 6
4 8
6 7
8 9
8 10
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18 20
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21 22

49
src/data/amber_q/HP2.frg
View file

@ -1,49 +0,0 @@
# This is an automatically generated fragment file
#
$HP2
22 1 1 0
HP2
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1 3
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8 9
8 10
8 11
11 12
11 13
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19 20
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19 22

57
src/data/amber_q/HP3.frg
View file

@ -1,57 +0,0 @@
# This is an automatically generated fragment file
#
$HP3
26 1 1 0
HP3
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3 OR OS 0 0 0 1 1 -0.229481 0.000000
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1 3
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47
src/data/amber_q/HP4.frg
View file

@ -1,47 +0,0 @@
# 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
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2 O1 OG 3 0 0 1 1 0.000000 0.000000
3 OR OS 0 0 0 1 1 -0.300000 0.000000
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1 2
1 3
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4 7
6 10
6 11
6 12
8 9
8 17
10 13
10 14
13 15
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15 17
15 20
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245
src/data/amber_q/HP4.sgm
View file

@ -1,245 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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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

65
src/data/amber_q/HP5.frg
View file

@ -1,65 +0,0 @@
# 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

373
src/data/amber_q/HP5.sgm
View file

@ -1,373 +0,0 @@
# 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

41
src/data/amber_q/HPD.frg
View file

@ -1,41 +0,0 @@
# 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

38
src/data/amber_q/HXO.frg
View file

@ -1,38 +0,0 @@
# 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

16
src/data/amber_q/IPS.frg
View file

@ -1,16 +0,0 @@
# 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

57
src/data/amber_q/KD1.frg
View file

@ -1,57 +0,0 @@
# 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

59
src/data/amber_q/KD2.frg
View file

@ -1,59 +0,0 @@
# 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

59
src/data/amber_q/KD3.frg
View file

@ -1,59 +0,0 @@
# 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

55
src/data/amber_q/KD4.frg
View file

@ -1,55 +0,0 @@
# 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
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1 2
1 3
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4 5
4 14
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307
src/data/amber_q/KD4.sgm
View file

@ -1,307 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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0.000000
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61
src/data/amber_q/KD5.frg
View file

@ -1,61 +0,0 @@
# 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
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9 C4 CT 0 0 0 1 1 0.250000 0.000000
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1 3
1 5
4 5
4 17
5 6
6 7
6 8
6 9
9 10
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9 13
11 12
13 14
13 15
13 17
15 16
17 18
17 19
19 20
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23 25
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26 27

353
src/data/amber_q/KD5.sgm
View file

@ -1,353 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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43
src/data/amber_q/KDN.frg
View file

@ -1,43 +0,0 @@
# 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
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61
src/data/amber_q/LCX.frg
View file

@ -1,61 +0,0 @@
# 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
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LCX
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1 2
3 7
3 5
3 4
5 6
7 10
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7 8
10 13
10 12
10 11
13 16
13 15
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16 19
16 18
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177
src/data/amber_q/LPO.sgm
View file

@ -1,177 +0,0 @@
# This is an automatically generated segment file
#
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401
src/data/amber_q/MA2.sgm
View file

@ -1,401 +0,0 @@
# This is an automatically generated segment file
#
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411
src/data/amber_q/MA3.sgm
View file

@ -1,411 +0,0 @@
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423
src/data/amber_q/MA4.sgm
View file

@ -1,423 +0,0 @@
# This is an automatically generated segment file
#
4.600000
33 33 57 81 5 0 1 1
0.000000
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45
src/data/amber_q/MAN.frg
View file

@ -1,45 +0,0 @@
# This is an automatically generated fragment file
#
$MAN
20 1 1 0
MAN
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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
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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
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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

16
src/data/amber_q/NH4.frg
View file

@ -1,16 +0,0 @@
# 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

Some files were not shown because too many files have changed in this diff Show more