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486 changed files with 563 additions and 59808 deletions
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113
.gitignore vendored
View file

@ -1,115 +1,32 @@
.vscode
bin/
build/
include/
lib/
### C ###
# Prerequisites
*.d
# Compiled Object files
*.o
*.ko
*.elf
*.obj
*.slo
# Linker output
*.ilk
*.map
*.exp
*.lo
*.o
*.obj
# Precompiled Headers
*.gch
*.pch
# Libraries
*.dll
# Compiled Dynamic libraries
*.so
*.so.*
*.dylib
*.lib
*.a
*.la
*.lo
*.dll
# Fortran module files
*.mod
*.smod
# Compiled Static libraries
*.lai
*.la
*.a
*.lib
# Executables
*.exe
*.out # output files
*.out
*.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

40
Makefile
View file

@ -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)

16
src/Makefile
View file

@ -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 $@

71
src/basis/getlibr.py Executable file → Normal file
View file

@ -1,35 +1,26 @@
#!/usr/bin/python3
#!/usr/bin/env python3
# This script downloads the basis set library data from www.basissetexchange.org
# into the directory $NWCHEM_TOP/src/basis/libraries.bse
# To 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/
# to use, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/
# Requires the installation of the python env. from
# https://github.com/MolSSI-BSE/basis_set_exchange
# 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']
for bas_name in all_bs:
#get version and list of elements
version_bs = md[bas_name]['latest_version']
elements_list = md[bas_name]['versions'][version_bs]['elements']
#open file
# get rid of asterisks
file_name = bas_name.replace("*","s")
@ -42,38 +33,19 @@ def writebs(md, bas_name, summary_file, get_aux=0):
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')
output_file.write('# Data downloaded at '+today+'\n')
output_file.write('# '+bas_name+' version number '+version_bs+'\n')
output_file.write('# Description: '+md[bas_name]['description']+'\n')
output_file.write('# Role: '+md[bas_name]['role']+'\n')
output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# '))
output_file.write('# \n')
for element in elements_list:
#element='h'
try:
bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True, get_aux=get_aux)
bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True)
except:
# print("failed for"+element)
pass
@ -82,22 +54,11 @@ def writebs(md, bas_name, summary_file, get_aux=0):
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)
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
print("end")
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")

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
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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
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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
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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
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17 4 10 11 0 0
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18 4 10 12 0 0
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19 11 10 12 0 0
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20 10 12 13 0 0
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21 10 12 14 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
0.000000 0.00000E+00
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
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 1 16 12 0 0
0.000000 0.00000E+00
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
21 21 37 56 0 0 1 1
0.000000
1 C1 3 0 0 1 1
EC 0.041291 0.000000
2 H1 0 0 0 1 1
H2 0.170645 0.000000
3 OR 0 0 0 1 1
OS -0.365330 0.000000
4 C2 0 0 0 1 1
CT 0.081809 0.000000
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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
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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
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21 22

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

@ -1,287 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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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
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1 2
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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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src/data/amber_q/GL7.frg
View file

@ -1,51 +0,0 @@
# This is an automatically generated fragment file
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# Atomic partial charges are crude guestimations
#
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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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16 14 15 0 0
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18 16 18 0 0
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22 21 22 0 0
0.000000 0.00000E+00
1 2 1 3 0 0
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2 2 1 4 0 0
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3 3 1 4 0 0
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4 1 3 16 0 0
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5 1 4 5 0 0
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6 1 4 6 0 0
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7 1 4 8 0 0
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8 5 4 6 0 0
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9 5 4 8 0 0
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10 6 4 8 0 0
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11 4 6 7 0 0
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12 4 8 9 0 0
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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
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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
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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
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24 14 12 16 0 0
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26 3 16 12 0 0
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27 3 16 17 0 0
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28 3 16 18 0 0
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29 12 16 17 0 0
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31 17 16 18 0 0
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32 16 18 19 0 0
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33 16 18 20 0 0
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34 16 18 21 0 0
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35 19 18 20 0 0
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36 19 18 21 0 0
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37 20 18 21 0 0
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38 18 21 22 0 0
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1 2 1 3 16 0 0
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2 4 1 3 16 0 0
0 0.000000 0.00000E+00
3 2 1 4 5 0 0
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6 3 1 4 5 0 0
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9 1 3 16 12 0 0
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11 1 3 16 18 0 0
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21 6 4 8 9 0 0
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22 6 4 8 10 0 0
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23 6 4 8 12 0 0
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24 4 8 10 11 0 0
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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
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28 4 8 12 14 0 0
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29 4 8 12 16 0 0
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30 9 8 12 13 0 0
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33 10 8 12 13 0 0
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36 8 12 14 15 0 0
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37 13 12 14 15 0 0
0 0.000000 0.00000E+00
38 16 12 14 15 0 0
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39 8 12 16 3 0 0
0 0.000000 0.00000E+00
40 8 12 16 17 0 0
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41 8 12 16 18 0 0
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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
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0 0.000000 0.00000E+00
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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
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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
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16 13 15 0 0
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17 15 16 0 0
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0.000000 0.00000E+00
21 20 21 0 0
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28 24 27 0 0
0.000000 0.00000E+00
29 28 29 0 0
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30 28 30 0 0
0.000000 0.00000E+00
1 2 1 3 0 0
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3 2 1 5 0 0
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11 6 5 7 0 0
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0.000000 0.00000E+00
13 7 5 20 0 0
0.000000 0.00000E+00
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18 8 7 10 0 0
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0.000000 0.00000E+00
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0.000000 0.00000E+00
22 7 10 13 0 0
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23 11 10 12 0 0
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24 11 10 13 0 0
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25 12 10 13 0 0
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26 4 13 10 0 0
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27 4 13 14 0 0
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29 10 13 14 0 0
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31 14 13 15 0 0
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32 13 15 16 0 0
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33 13 15 17 0 0
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34 13 15 18 0 0
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35 16 15 17 0 0
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36 16 15 18 0 0
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37 17 15 18 0 0
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38 15 18 19 0 0
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39 5 20 21 0 0
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40 5 20 22 0 0
0.000000 0.00000E+00
41 21 20 22 0 0
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42 20 22 23 0 0
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43 20 22 24 0 0
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44 20 22 28 0 0
0.000000 0.00000E+00
45 23 22 24 0 0
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46 23 22 28 0 0
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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
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50 22 24 27 0 0
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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
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55 22 28 30 0 0
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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
0 0.000000 0.00000E+00
35 8 7 10 12 0 0
0 0.000000 0.00000E+00
36 8 7 10 13 0 0
0 0.000000 0.00000E+00
37 9 7 10 11 0 0
0 0.000000 0.00000E+00
38 9 7 10 12 0 0
0 0.000000 0.00000E+00
39 9 7 10 13 0 0
0 0.000000 0.00000E+00
40 7 10 13 4 0 0
0 0.000000 0.00000E+00
41 7 10 13 14 0 0
0 0.000000 0.00000E+00
42 7 10 13 15 0 0
0 0.000000 0.00000E+00
43 11 10 13 4 0 0
0 0.000000 0.00000E+00
44 11 10 13 14 0 0
0 0.000000 0.00000E+00
45 11 10 13 15 0 0
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46 12 10 13 4 0 0
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47 12 10 13 14 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
0 0.000000 0.00000E+00
56 14 13 15 17 0 0
0 0.000000 0.00000E+00
57 14 13 15 18 0 0
0 0.000000 0.00000E+00
58 13 15 18 19 0 0
0 0.000000 0.00000E+00
59 16 15 18 19 0 0
0 0.000000 0.00000E+00
60 17 15 18 19 0 0
0 0.000000 0.00000E+00
61 5 20 22 23 0 0
0 0.000000 0.00000E+00
62 5 20 22 24 0 0
0 0.000000 0.00000E+00
63 5 20 22 28 0 0
0 0.000000 0.00000E+00
64 21 20 22 23 0 0
0 0.000000 0.00000E+00
65 21 20 22 24 0 0
0 0.000000 0.00000E+00
66 21 20 22 28 0 0
0 0.000000 0.00000E+00
67 20 22 24 25 0 0
0 0.000000 0.00000E+00
68 20 22 24 26 0 0
0 0.000000 0.00000E+00
69 20 22 24 27 0 0
0 0.000000 0.00000E+00
70 23 22 24 25 0 0
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71 23 22 24 26 0 0
0 0.000000 0.00000E+00
72 23 22 24 27 0 0
0 0.000000 0.00000E+00
73 28 22 24 25 0 0
0 0.000000 0.00000E+00
74 28 22 24 26 0 0
0 0.000000 0.00000E+00
75 28 22 24 27 0 0
0 0.000000 0.00000E+00
76 20 22 28 29 0 0
0 0.000000 0.00000E+00
77 20 22 28 30 0 0
0 0.000000 0.00000E+00
78 23 22 28 29 0 0
0 0.000000 0.00000E+00
79 23 22 28 30 0 0
0 0.000000 0.00000E+00
80 24 22 28 29 0 0
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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
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1 3
1 4
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5 6
5 7
5 8
5 9
9 10
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10 12
10 13
13 14
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17 18
17 19
17 20
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20 21
20 22
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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
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2 O1 O 0 0 0 1 1 -0.656819 0.000000
3 C2 CT 0 0 0 1 1 -0.065272 0.000000
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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
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10 13
13 14
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169
src/data/amber_q/HDH.sgm
View file

@ -1,169 +0,0 @@
# This is an automatically generated segment file
#
4.600000
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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
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1 2
1 3
3 4
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3 6
6 7
6 8
6 9
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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
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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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1 NZ 0 0 0 1 1
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H 0.291236 0.000000
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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
1FE FE 3 0 0 1 1 1.740000 0.000000
2 N A NP 0 0 0 1 1 -0.840000 0.000000
3 C1A CC 0 4 0 1 1 0.580000 0.000000
4 C2A CB 0 4 0 1 1 -0.280000 0.000000
5 CAA CT 0 0 0 1 1 -0.100000 0.000000
62HAA HC 0 0 0 1 1 0.100000 0.000000
73HAA HC 0 0 0 1 1 0.100000 0.000000
8 CBA CT 0 0 0 1 1 -0.200000 0.000000
92HBA HC 0 0 0 1 1 0.100000 0.000000
103HBA HC 0 0 0 1 1 0.100000 0.000000
11 CGA C 0 1 0 1 1 0.350000 0.000000
12 O1A O2 0 0 0 1 1 -0.575000 0.000000
13 O2A O2 0 0 0 1 1 -0.575000 0.000000
14 C3A CB 0 4 0 1 1 -0.280000 0.000000
15 CMA CT 0 0 0 1 1 -0.150000 0.000000
162HMA HC 0 0 0 1 1 0.100000 0.000000
173HMA HC 0 0 0 1 1 0.100000 0.000000
184HMA HC 0 0 0 1 1 0.100000 0.000000
19 C4A CC 0 4 0 1 1 0.580000 0.000000
20 CHB CD 0 1 0 1 1 -0.640000 0.000000
21 HHB HC 0 0 0 1 1 0.130000 0.000000
22 C1B CC 0 4 0 1 1 0.580000 0.000000
23 N B NO 0 0 0 1 1 -0.840000 0.000000
24 C2B CB 0 4 0 1 1 -0.280000 0.000000
25 CMB CT 0 0 0 1 1 -0.150000 0.000000
262HMB HC 0 0 0 1 1 0.100000 0.000000
273HMB HC 0 0 0 1 1 0.100000 0.000000
284HMB HC 0 0 0 1 1 0.100000 0.000000
29 C3B CB 0 4 0 1 1 -0.280000 0.000000
30 CAB CY 0 0 0 1 1 -0.100000 0.000000
31 HVB HC 0 0 0 1 1 0.130000 0.000000
32 CBB CX 0 0 0 1 1 -0.200000 0.000000
332HV2 HC 0 0 0 1 1 0.100000 0.000000
343HV2 HC 0 0 0 1 1 0.100000 0.000000
35 C4B CC 0 4 0 1 1 0.580000 0.000000
36 CHC CD 0 1 0 1 1 -0.640000 0.000000
37 HHC HC 0 0 0 1 1 0.130000 0.000000
38 C1C CC 0 4 0 1 1 0.580000 0.000000
39 N C NP 0 0 0 1 1 -0.840000 0.000000
40 C2C CB 0 4 0 1 1 -0.280000 0.000000
41 CMC CT 0 0 0 1 1 -0.150000 0.000000
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433HMC HC 0 0 0 1 1 0.100000 0.000000
444HMC HC 0 0 0 1 1 0.100000 0.000000
45 C3C CB 0 4 0 1 1 -0.280000 0.000000
46 CAC CY 0 0 0 1 1 -0.100000 0.000000
47 HVC HC 0 0 0 1 1 0.130000 0.000000
48 CBC CX 0 0 0 1 1 -0.200000 0.000000
492HV4 HC 0 0 0 1 1 0.100000 0.000000
503HV4 HC 0 0 0 1 1 0.100000 0.000000
51 C4C CC 0 4 0 1 1 0.580000 0.000000
52 CHD CD 0 1 0 1 1 -0.640000 0.000000
53 HHD HC 0 0 0 1 1 0.130000 0.000000
54 C1D CC 0 4 0 1 1 0.580000 0.000000
55 N D NO 0 0 0 1 1 -0.840000 0.000000
56 C2D CB 0 4 0 1 1 -0.280000 0.000000
57 CMD CT 0 0 0 1 1 -0.150000 0.000000
582HMD HC 0 0 0 1 1 0.100000 0.000000
593HMD HC 0 0 0 1 1 0.100000 0.000000
604HMD HC 0 0 0 1 1 0.100000 0.000000
61 C3D CB 0 4 0 1 1 -0.280000 0.000000
62 C4D CC 0 4 0 1 1 0.580000 0.000000
63 CHA CD 0 1 0 1 1 -0.640000 0.000000
64 HHA HC 0 0 0 1 1 0.130000 0.000000
65 CAD CT 0 0 0 1 1 -0.100000 0.000000
662HAD HC 0 0 0 1 1 0.100000 0.000000
673HAD HC 0 0 0 1 1 0.100000 0.000000
68 CBD CT 0 0 0 1 1 -0.200000 0.000000
692HBD HC 0 0 0 1 1 0.100000 0.000000
703HBD HC 0 0 0 1 1 0.100000 0.000000
71 CGD C 0 1 0 1 1 0.350000 0.000000
72 O1D O2 0 0 0 1 1 -0.575000 0.000000
73 O2D O2 0 0 0 1 1 -0.575000 0.000000
1 2
1 23
1 39
1 55
2 3
2 19
3 4
3 63
4 5
4 14
5 6
5 7
5 8
8 9
8 10
8 11
11 12
11 13
14 15
14 19
15 16
15 17
15 18
19 20
20 21
20 22
22 23
22 24
23 35
24 25
24 29
25 26
25 27
25 28
29 30
29 35
30 31
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32 33
32 34
35 36
36 37
36 38
38 39
38 40
39 51
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40 45
41 42
41 43
41 44
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46 47
46 48
48 49
48 50
51 52
52 53
52 54
54 55
54 56
55 62
56 57
56 61
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57 60
61 62
61 65
62 63
63 64
65 66
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68 71
71 72
71 73

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
HEP
1 C1 CT 3 0 0 1 1 -0.100000 0.000000
22H1 HC 0 0 0 1 1 0.050000 0.000000
33H1 HC 0 0 0 1 1 0.050000 0.000000
4 C2 CT 0 0 0 1 1 -0.100000 0.000000
52H2 HC 0 0 0 1 1 0.050000 0.000000
63H2 HC 0 0 0 1 1 0.050000 0.000000
7 C3 CT 0 0 0 1 1 -0.100000 0.000000
82H3 HC 0 0 0 1 1 0.050000 0.000000
93H3 HC 0 0 0 1 1 0.050000 0.000000
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153H5 HC 0 0 0 1 1 0.050000 0.000000
16 C6 CT 0 0 0 1 1 -0.100000 0.000000
172H6 HC 0 0 0 1 1 0.050000 0.000000
183H6 HC 0 0 0 1 1 0.050000 0.000000
19 C7 CT 0 0 0 1 1 -0.150000 0.000000
202H7 HC 0 0 0 1 1 0.050000 0.000000
213H7 HC 0 0 0 1 1 0.050000 0.000000
224H7 HC 0 0 0 1 1 0.050000 0.000000
1 2
1 3
1 4
4 5
4 6
4 7
7 8
7 9
7 10
10 11
10 12
10 13
13 14
13 15
13 16
16 17
16 18
16 19
19 20
19 21
19 22

271
src/data/amber_q/HEP.sgm
View file

@ -1,271 +0,0 @@
# This is an automatically generated segment file
#
4.600000
22 21 39 51 0 0 1 1
0.000000
1 C1 3 0 0 1 1
CT -0.100000 0.000000
22H1 0 0 0 1 1
HC 0.050000 0.000000
33H1 0 0 0 1 1
HC 0.050000 0.000000
4 C2 0 0 0 1 1
CT -0.100000 0.000000
52H2 0 0 0 1 1
HC 0.050000 0.000000
63H2 0 0 0 1 1
HC 0.050000 0.000000
7 C3 0 0 0 1 1
CT -0.100000 0.000000
82H3 0 0 0 1 1
HC 0.050000 0.000000
93H3 0 0 0 1 1
HC 0.050000 0.000000
10 C4 0 0 0 1 1
CT -0.100000 0.000000
112H4 0 0 0 1 1
HC 0.050000 0.000000
123H4 0 0 0 1 1
HC 0.050000 0.000000
13 C5 0 0 0 1 1
CT -0.100000 0.000000
142H5 0 0 0 1 1
HC 0.050000 0.000000
153H5 0 0 0 1 1
HC 0.050000 0.000000
16 C6 0 0 0 1 1
CT -0.100000 0.000000
172H6 0 0 0 1 1
HC 0.050000 0.000000
183H6 0 0 0 1 1
HC 0.050000 0.000000
19 C7 0 0 0 1 1
CT -0.150000 0.000000
202H7 0 0 0 1 1
HC 0.050000 0.000000
213H7 0 0 0 1 1
HC 0.050000 0.000000
224H7 0 0 0 1 1
HC 0.050000 0.000000
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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
1 C1 AC 3 0 0 1 1 -0.239301 0.000000
2 H1 H2 0 0 0 1 1 0.241979 0.000000
3 OR OS 0 0 0 1 1 -0.415373 0.000000
4 C2 CT 0 0 0 1 1 0.042475 0.000000
5 H2 H1 0 0 0 1 1 0.077985 0.000000
6 O2 OH 0 0 0 1 1 -0.647450 0.000000
7 HO2 HO 0 0 0 1 1 0.482404 0.000000
8 C3 CT 0 0 0 1 1 0.010480 0.000000
9 H3 H1 0 0 0 1 1 0.111498 0.000000
10 C4 CT 4 0 0 1 1 0.436393 0.000000
11 H4 H1 0 0 0 1 1 0.091286 0.000000
12 C5 CT 0 0 0 1 1 0.036980 0.000000
13 H5 H1 0 0 0 1 1 0.127831 0.000000
14 C6 CT 0 0 0 1 1 0.076400 0.000000
15 H6 H1 0 0 0 1 1 0.041079 0.000000
16 O6 OH 0 0 0 1 1 -0.406753 0.000000
17 HO6 HO 0 0 0 1 1 0.097859 0.000000
18 C7 CT 0 0 0 1 1 0.028666 0.000000
192H7 H1 0 0 0 1 1 0.132550 0.000000
203H7 H1 0 0 0 1 1 0.132550 0.000000
21 O7 OH 0 0 0 1 1 -0.668904 0.000000
22 HO7 HO 0 0 0 1 1 0.412396 0.000000
23 O3 OG 5 0 0 1 1 -0.203030 0.000000
1 2
1 3
1 4
3 12
4 5
4 6
4 8
6 7
8 9
8 10
8 23
10 11
10 12
12 13
12 14
14 15
14 16
14 18
16 17
18 19
18 20
18 21
21 22

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
1 C1 AC 3 0 0 1 1 -0.010164 0.000000
2 H1 H2 0 0 0 1 1 0.240927 0.000000
3 OR OS 0 0 0 1 1 -0.252805 0.000000
4 C2 CT 0 0 0 1 1 -0.006072 0.000000
5 H2 H1 0 0 0 1 1 0.134561 0.000000
6 O2 OH 0 0 0 1 1 -0.610787 0.000000
7 HO2 HO 0 0 0 1 1 0.560263 0.000000
8 C3 CT 0 0 0 1 1 0.033998 0.000000
9 H3 H1 0 0 0 1 1 0.234578 0.000000
10 O3 OG 4 0 0 1 1 -0.082473 0.000000
11 C4 CT 5 0 0 1 1 -0.836484 0.000000
12 H4 H1 0 0 0 1 1 0.429570 0.000000
13 C5 CT 0 0 0 1 1 -0.033855 0.000000
14 H5 H1 0 0 0 1 1 0.246413 0.000000
15 C6 CT 0 0 0 1 1 0.209473 0.000000
16 H6 H1 0 0 0 1 1 0.201307 0.000000
17 O6 OH 0 0 0 1 1 -0.639374 0.000000
18 HO6 HO 0 0 0 1 1 0.424900 0.000000
19 C7 CT 0 0 0 1 1 0.105186 0.000000
202H7 H1 0 0 0 1 1 0.004214 0.000000
213H7 H1 0 0 0 1 1 0.004214 0.000000
22 O7 OG 6 0 0 1 1 -0.357590 0.000000
1 2
1 3
1 4
3 13
4 5
4 6
4 8
6 7
8 9
8 10
8 11
11 12
11 13
13 14
13 15
15 16
15 17
15 19
17 18
19 20
19 21
19 22

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
1 C1 AC 3 0 0 1 1 -0.181949 0.000000
2 H1 H2 0 0 0 1 1 0.216044 0.000000
3 OR OS 0 0 0 1 1 -0.229481 0.000000
4 C2 CT 0 0 0 1 1 0.277637 0.000000
5 H2 H1 0 0 0 1 1 0.089495 0.000000
6 O2 OH 0 0 0 1 1 -0.894528 0.000000
7 HO2 HO 0 0 0 1 1 0.594996 0.000000
8 C3 CT 0 0 0 1 1 0.029277 0.000000
9 H3 H1 0 0 0 1 1 0.136134 0.000000
10 O3 OH 0 0 0 1 1 -0.774477 0.000000
11 HO3 HO 0 0 0 1 1 0.501260 0.000000
12 C4 CT 0 0 0 1 1 0.451101 0.000000
13 H4 H1 0 0 0 1 1 0.070853 0.000000
14 O4 OH 0 0 0 1 1 -0.974205 0.000000
15 HO4 HO 0 0 0 1 1 0.572360 0.000000
16 C5 CT 0 0 0 1 1 0.055923 0.000000
17 H5 H1 0 0 0 1 1 0.029069 0.000000
18 C6 CT 0 0 0 1 1 0.244883 0.000000
19 H6 H1 0 0 0 1 1 0.089606 0.000000
20 O6 OH 0 0 0 1 1 -0.621510 0.000000
21 HO6 HO 0 0 0 1 1 0.412202 0.000000
22 C7 CT 0 0 0 1 1 0.054009 0.000000
232H7 H1 0 0 0 1 1 0.050176 0.000000
243H7 H1 0 0 0 1 1 0.050176 0.000000
25 O7 OH 0 0 0 1 1 -0.708732 0.000000
26 HO7 HO 0 0 0 1 1 0.459681 0.000000
1 2
1 3
1 4
3 16
4 5
4 6
4 8
6 7
8 9
8 10
8 12
10 11
12 13
12 14
12 16
14 15
16 17
16 18
18 19
18 20
18 22
20 21
22 23
22 24
22 25
25 26

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
1 C1 AC 0 0 0 1 1 0.000000 0.000000
2 O1 OG 3 0 0 1 1 0.000000 0.000000
3 OR OS 0 0 0 1 1 -0.300000 0.000000
4 C2 CT 4 0 0 1 1 -0.050000 0.000000
5 H2 H2 0 0 0 1 1 0.000000 0.000000
6 C3 CT 0 0 0 1 1 0.250000 0.000000
7 H3 H1 0 0 0 1 1 0.050000 0.000000
8 O3 OH 0 0 0 1 1 -0.490000 0.000000
9 HO3 HO 0 0 0 1 1 0.190000 0.000000
10 C4 CT 5 0 0 1 1 -0.050000 0.000000
11 H4 H1 0 0 0 1 1 0.050000 0.000000
12 O4 OG 6 0 0 1 1 -0.300000 0.000000
13 C5 CT 0 0 0 1 1 0.250000 0.000000
14 H5 H1 0 0 0 1 1 0.050000 0.000000
15 C6 CT 7 0 0 1 1 -0.050000 0.000000
16 H6 H1 0 0 0 1 1 0.050000 0.000000
17 C7 CT 0 0 0 1 1 0.200000 0.000000
182H7 H1 0 0 0 1 1 0.050000 0.000000
193H7 H1 0 0 0 1 1 0.050000 0.000000
20 H7 H1 0 0 0 1 1 0.050000 0.000000
1 2
1 3
1 4
1 5
3 13
4 6
4 7
6 10
6 11
6 12
8 9
8 17
10 13
10 14
13 15
13 16
15 17
15 20
17 18
17 19

245
src/data/amber_q/HP4.sgm
View file

@ -1,245 +0,0 @@
# This is an automatically generated segment file
#
4.600000
20 20 35 45 0 0 1 1
0.000000
1 C1 0 0 0 1 1
AC 0.466075 0.000000
2 O1 3 0 0 1 1
OG -0.079506 0.000000
3 OR 0 0 0 1 1
OS -0.455698 0.000000
4 C2 4 0 0 1 1
CT -0.157271 0.000000
5 H2 0 0 0 1 1
H2 -0.029617 0.000000
6 C3 0 0 0 1 1
CT 0.108269 0.000000
7 H3 0 0 0 1 1
H1 0.167743 0.000000
8 O3 0 0 0 1 1
OH -0.608041 0.000000
9 HO3 0 0 0 1 1
HO 0.393759 0.000000
10 C4 5 0 0 1 1
CT -0.153131 0.000000
11 H4 0 0 0 1 1
H1 0.117228 0.000000
12 O4 6 0 0 1 1
OG -0.251176 0.000000
13 C5 0 0 0 1 1
CT -0.415204 0.000000
14 H5 0 0 0 1 1
H1 0.251985 0.000000
15 C6 7 0 0 1 1
CT 0.480601 0.000000
16 H6 0 0 0 1 1
H1 0.059996 0.000000
17 C7 0 0 0 1 1
CT -0.114932 0.000000
182H7 0 0 0 1 1
H1 0.089587 0.000000
193H7 0 0 0 1 1
H1 0.089587 0.000000
20 H7 0 0 0 1 1
H1 0.039746 0.000000
1 1 2 0 0
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42 13 15 17 19 0 0
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45 20 15 17 19 0 0
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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
5 C2 AC 3 0 0 1 1 0.000000 0.000000
6 C3 CT 0 0 0 1 1 -0.100000 0.000000
72H3 HC 0 0 0 1 1 0.050000 0.000000
83H3 HC 0 0 0 1 1 0.050000 0.000000
9 C4 CT 0 0 0 1 1 0.250000 0.000000
10 H4 H1 0 0 0 1 1 0.050000 0.000000
11 O4 OG 4 0 0 1 1 -0.300000 0.000000
12 C5 CT 5 0 0 1 1 -0.050000 0.000000
13 H5 H1 0 0 0 1 1 0.050000 0.000000
14 C6 CT 0 0 0 1 1 0.250000 0.000000
15 H6 H1 0 0 0 1 1 0.050000 0.000000
16 C7 CT 0 0 0 1 1 0.250000 0.000000
17 H7 H1 0 0 0 1 1 0.050000 0.000000
18 O7 OH 0 0 0 1 1 -0.490000 0.000000
19 HO7 HO 0 0 0 1 1 0.190000 0.000000
20 C8 CT 0 0 0 1 1 0.200000 0.000000
212H8 H1 0 0 0 1 1 0.050000 0.000000
223H8 H1 0 0 0 1 1 0.050000 0.000000
23 O8 OH 0 0 0 1 1 -0.490000 0.000000
24 HO8 HO 0 0 0 1 1 0.190000 0.000000
1 2
1 3
1 5
4 5
4 14
5 6
6 7
6 8
6 9
9 10
9 11
9 12
12 13
12 14
14 15
14 16
16 17
16 18
16 20
18 19
20 21
20 22
20 23
23 24

307
src/data/amber_q/KD4.sgm
View file

@ -1,307 +0,0 @@
# This is an automatically generated segment file
#
4.600000
24 24 42 60 1 0 1 1
0.000000
1 C1 0 1 0 1 1
C 0.473407 0.000000
2 O1 0 0 0 1 1
O2 -0.736704 0.000000
3 O 0 0 0 1 1
O2 -0.736704 0.000000
4 OR 0 0 0 1 1
OS -0.605275 0.000000
5 C2 3 0 0 1 1
AC 0.339543 0.000000
6 C3 0 0 0 1 1
CT -0.018770 0.000000
72H3 0 0 0 1 1
HC 0.108290 0.000000
83H3 0 0 0 1 1
HC 0.108290 0.000000
9 C4 0 0 0 1 1
CT 0.015472 0.000000
10 H4 0 0 0 1 1
H1 0.171605 0.000000
11 O4 4 0 0 1 1
OG -0.263850 0.000000
12 C5 5 0 0 1 1
CT -0.362258 0.000000
13 H5 0 0 0 1 1
H1 0.255752 0.000000
14 C6 0 0 0 1 1
CT -0.133148 0.000000
15 H6 0 0 0 1 1
H1 0.128242 0.000000
16 C7 0 0 0 1 1
CT 0.603049 0.000000
17 H7 0 0 0 1 1
H1 0.023453 0.000000
18 O7 0 0 0 1 1
OH -0.728146 0.000000
19 HO7 0 0 0 1 1
HO 0.466143 0.000000
20 C8 0 0 0 1 1
CT 0.001132 0.000000
212H8 0 0 0 1 1
H1 0.100000 0.000000
223H8 0 0 0 1 1
H1 0.100000 0.000000
23 O8 0 0 0 1 1
OH -0.728146 0.000000
24 HO8 0 0 0 1 1
HO 0.418623 0.000000
1 1 2 0 0
0.000000 0.00000E+00
2 1 3 0 0
0.000000 0.00000E+00
3 1 5 0 0
0.000000 0.00000E+00
4 4 5 0 0
0.000000 0.00000E+00
5 4 14 0 0
0.000000 0.00000E+00
6 5 6 0 0
0.000000 0.00000E+00
7 6 7 0 0
0.000000 0.00000E+00
8 6 8 0 0
0.000000 0.00000E+00
9 6 9 0 0
0.000000 0.00000E+00
10 9 10 0 0
0.000000 0.00000E+00
11 9 11 0 0
0.000000 0.00000E+00
12 9 12 0 0
0.000000 0.00000E+00
13 12 13 0 0
0.000000 0.00000E+00
14 12 14 0 0
0.000000 0.00000E+00
15 14 15 0 0
0.000000 0.00000E+00
16 14 16 0 0
0.000000 0.00000E+00
17 16 17 0 0
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18 16 18 0 0
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19 16 20 0 0
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21 20 21 0 0
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22 20 22 0 0
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23 20 23 0 0
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24 23 24 0 0
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1 2 1 3 0 0
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2 2 1 5 0 0
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3 3 1 5 0 0
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4 5 4 14 0 0
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5 1 5 4 0 0
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6 1 5 6 0 0
0.000000 0.00000E+00
7 4 5 6 0 0
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8 5 6 7 0 0
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0.000000 0.00000E+00
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0.000000 0.00000E+00
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31 14 16 20 0 0
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32 17 16 18 0 0
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33 17 16 20 0 0
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34 18 16 20 0 0
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36 16 20 21 0 0
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0.000000 0.00000E+00
1 2 1 5 4 0 0
0 0.000000 0.00000E+00
2 2 1 5 6 0 0
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3 3 1 5 4 0 0
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4 3 1 5 6 0 0
0 0.000000 0.00000E+00
5 14 4 5 1 0 0
0 0.000000 0.00000E+00
6 14 4 5 6 0 0
0 0.000000 0.00000E+00
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0 0.000000 0.00000E+00
8 5 4 14 15 0 0
0 0.000000 0.00000E+00
9 5 4 14 16 0 0
0 0.000000 0.00000E+00
10 1 5 6 7 0 0
0 0.000000 0.00000E+00
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13 4 5 6 7 0 0
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15 4 5 6 9 0 0
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16 5 6 9 10 0 0
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17 5 6 9 11 0 0
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18 5 6 9 12 0 0
0 0.000000 0.00000E+00
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0 0.000000 0.00000E+00
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0 0.000000 0.00000E+00
22 8 6 9 10 0 0
0 0.000000 0.00000E+00
23 8 6 9 11 0 0
0 0.000000 0.00000E+00
24 8 6 9 12 0 0
0 0.000000 0.00000E+00
25 6 9 12 13 0 0
0 0.000000 0.00000E+00
26 6 9 12 14 0 0
0 0.000000 0.00000E+00
27 10 9 12 13 0 0
0 0.000000 0.00000E+00
28 10 9 12 14 0 0
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29 11 9 12 13 0 0
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0 0.000000 0.00000E+00
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0 0.000000 0.00000E+00
33 9 12 14 16 0 0
0 0.000000 0.00000E+00
34 13 12 14 4 0 0
0 0.000000 0.00000E+00
35 13 12 14 15 0 0
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37 4 14 16 17 0 0
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38 4 14 16 18 0 0
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39 4 14 16 20 0 0
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40 12 14 16 17 0 0
0 0.000000 0.00000E+00
41 12 14 16 18 0 0
0 0.000000 0.00000E+00
42 12 14 16 20 0 0
0 0.000000 0.00000E+00
43 15 14 16 17 0 0
0 0.000000 0.00000E+00
44 15 14 16 18 0 0
0 0.000000 0.00000E+00
45 15 14 16 20 0 0
0 0.000000 0.00000E+00
46 14 16 18 19 0 0
0 0.000000 0.00000E+00
47 17 16 18 19 0 0
0 0.000000 0.00000E+00
48 20 16 18 19 0 0
0 0.000000 0.00000E+00
49 14 16 20 21 0 0
0 0.000000 0.00000E+00
50 14 16 20 22 0 0
0 0.000000 0.00000E+00
51 14 16 20 23 0 0
0 0.000000 0.00000E+00
52 17 16 20 21 0 0
0 0.000000 0.00000E+00
53 17 16 20 22 0 0
0 0.000000 0.00000E+00
54 17 16 20 23 0 0
0 0.000000 0.00000E+00
55 18 16 20 21 0 0
0 0.000000 0.00000E+00
56 18 16 20 22 0 0
0 0.000000 0.00000E+00
57 18 16 20 23 0 0
0 0.000000 0.00000E+00
58 16 20 23 24 0 0
0 0.000000 0.00000E+00
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0 0.000000 0.00000E+00
60 22 20 23 24 0 0
0 0.000000 0.00000E+00
1 5 3 1 2 0 0
0 0.000000 0.00000E+00

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
72H3 HC 0 0 0 1 1 0.050000 0.000000
83H3 HC 0 0 0 1 1 0.050000 0.000000
9 C4 CT 0 0 0 1 1 0.250000 0.000000
10 H4 H1 0 0 0 1 1 0.050000 0.000000
11 O4 OH 0 0 0 1 1 -0.490000 0.000000
12 HO4 HO 0 0 0 1 1 0.190000 0.000000
13 C5 CT 0 0 0 1 1 0.250000 0.000000
14 H5 H1 0 0 0 1 1 0.050000 0.000000
15 O5 OH 0 0 0 1 1 -0.490000 0.000000
16 HO5 HO 0 0 0 1 1 0.190000 0.000000
17 C6 CT 0 0 0 1 1 0.250000 0.000000
18 H6 H1 0 0 0 1 1 0.050000 0.000000
19 C7 CT 0 0 0 1 1 0.250000 0.000000
20 H7 H1 0 0 0 1 1 0.050000 0.000000
21 O7 OH 0 0 0 1 1 -0.490000 0.000000
22 HO7 HO 0 0 0 1 1 0.190000 0.000000
23 C8 CT 0 0 0 1 1 0.200000 0.000000
242H8 H1 0 0 0 1 1 0.050000 0.000000
253H8 H1 0 0 0 1 1 0.050000 0.000000
26 O8 OH 0 0 0 1 1 -0.490000 0.000000
27 HO8 HO 0 0 0 1 1 0.190000 0.000000
1 2
1 3
1 5
4 5
4 17
5 6
6 7
6 8
6 9
9 10
9 11
9 13
11 12
13 14
13 15
13 17
15 16
17 18
17 19
19 20
19 21
19 23
21 22
23 24
23 25
23 26
26 27

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

@ -1,353 +0,0 @@
# This is an automatically generated segment file
#
4.600000
27 27 47 72 1 0 1 1
0.000000
1 C1 0 1 0 1 1
C 0.473407 0.000000
2 O1 0 0 0 1 1
O2 -0.736704 0.000000
3 O 0 0 0 1 1
O2 -0.736704 0.000000
4 OR 0 0 0 1 1
OS -0.605275 0.000000
5 C2 3 0 0 1 1
AC 0.339543 0.000000
6 C3 0 0 0 1 1
CT -0.018770 0.000000
72H3 0 0 0 1 1
HC 0.078388 0.000000
83H3 0 0 0 1 1
HC 0.078388 0.000000
9 C4 0 0 0 1 1
CT 0.015471 0.000000
10 H4 0 0 0 1 1
H1 0.080818 0.000000
11 O4 0 0 0 1 1
OH -0.646505 0.000000
12 HO4 0 0 0 1 1
HO 0.503250 0.000000
13 C5 0 0 0 1 1
CT -0.058856 0.000000
14 H5 0 0 0 1 1
H1 0.188953 0.000000
15 O5 0 0 0 1 1
OH -0.728146 0.000000
16 HO5 0 0 0 1 1
HO 0.508424 0.000000
17 C6 0 0 0 1 1
CT -0.133148 0.000000
18 H6 0 0 0 1 1
H1 0.141358 0.000000
19 C7 0 0 0 1 1
CT 0.603049 0.000000
20 H7 0 0 0 1 1
H1 0.023453 0.000000
21 O7 0 0 0 1 1
OH -0.728146 0.000000
22 HO7 0 0 0 1 1
HO 0.466143 0.000000
23 C8 0 0 0 1 1
CT 0.001132 0.000000
242H8 0 0 0 1 1
H1 0.100000 0.000000
253H8 0 0 0 1 1
H1 0.100000 0.000000
26 O8 0 0 0 1 1
OH -0.728146 0.000000
27 HO8 0 0 0 1 1
HO 0.418623 0.000000
1 1 2 0 0
0.000000 0.00000E+00
2 1 3 0 0
0.000000 0.00000E+00
3 1 5 0 0
0.000000 0.00000E+00
4 4 5 0 0
0.000000 0.00000E+00
5 4 17 0 0
0.000000 0.00000E+00
6 5 6 0 0
0.000000 0.00000E+00
7 6 7 0 0
0.000000 0.00000E+00
8 6 8 0 0
0.000000 0.00000E+00
9 6 9 0 0
0.000000 0.00000E+00
10 9 10 0 0
0.000000 0.00000E+00
11 9 11 0 0
0.000000 0.00000E+00
12 9 13 0 0
0.000000 0.00000E+00
13 11 12 0 0
0.000000 0.00000E+00
14 13 14 0 0
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15 13 15 0 0
0.000000 0.00000E+00
16 13 17 0 0
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17 15 16 0 0
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18 17 18 0 0
0.000000 0.00000E+00
19 17 19 0 0
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20 19 20 0 0
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21 19 21 0 0
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23 21 22 0 0
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26 23 26 0 0
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3 3 1 5 0 0
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4 5 4 17 0 0
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6 1 5 6 0 0
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10 5 6 9 0 0
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11 7 6 8 0 0
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0.000000 0.00000E+00
19 11 9 13 0 0
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25 14 13 17 0 0
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27 13 15 16 0 0
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29 4 17 18 0 0
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31 13 17 18 0 0
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32 13 17 19 0 0
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33 18 17 19 0 0
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1 2 1 5 4 0 0
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3 3 1 5 4 0 0
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4 3 1 5 6 0 0
0 0.000000 0.00000E+00
5 17 4 5 1 0 0
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7 5 4 17 13 0 0
0 0.000000 0.00000E+00
8 5 4 17 18 0 0
0 0.000000 0.00000E+00
9 5 4 17 19 0 0
0 0.000000 0.00000E+00
10 1 5 6 7 0 0
0 0.000000 0.00000E+00
11 1 5 6 8 0 0
0 0.000000 0.00000E+00
12 1 5 6 9 0 0
0 0.000000 0.00000E+00
13 4 5 6 7 0 0
0 0.000000 0.00000E+00
14 4 5 6 8 0 0
0 0.000000 0.00000E+00
15 4 5 6 9 0 0
0 0.000000 0.00000E+00
16 5 6 9 10 0 0
0 0.000000 0.00000E+00
17 5 6 9 11 0 0
0 0.000000 0.00000E+00
18 5 6 9 13 0 0
0 0.000000 0.00000E+00
19 7 6 9 10 0 0
0 0.000000 0.00000E+00
20 7 6 9 11 0 0
0 0.000000 0.00000E+00
21 7 6 9 13 0 0
0 0.000000 0.00000E+00
22 8 6 9 10 0 0
0 0.000000 0.00000E+00
23 8 6 9 11 0 0
0 0.000000 0.00000E+00
24 8 6 9 13 0 0
0 0.000000 0.00000E+00
25 6 9 11 12 0 0
0 0.000000 0.00000E+00
26 10 9 11 12 0 0
0 0.000000 0.00000E+00
27 13 9 11 12 0 0
0 0.000000 0.00000E+00
28 6 9 13 14 0 0
0 0.000000 0.00000E+00
29 6 9 13 15 0 0
0 0.000000 0.00000E+00
30 6 9 13 17 0 0
0 0.000000 0.00000E+00
31 10 9 13 14 0 0
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32 10 9 13 15 0 0
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33 10 9 13 17 0 0
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34 11 9 13 14 0 0
0 0.000000 0.00000E+00
35 11 9 13 15 0 0
0 0.000000 0.00000E+00
36 11 9 13 17 0 0
0 0.000000 0.00000E+00
37 9 13 15 16 0 0
0 0.000000 0.00000E+00
38 14 13 15 16 0 0
0 0.000000 0.00000E+00
39 17 13 15 16 0 0
0 0.000000 0.00000E+00
40 9 13 17 4 0 0
0 0.000000 0.00000E+00
41 9 13 17 18 0 0
0 0.000000 0.00000E+00
42 9 13 17 19 0 0
0 0.000000 0.00000E+00
43 14 13 17 4 0 0
0 0.000000 0.00000E+00
44 14 13 17 18 0 0
0 0.000000 0.00000E+00
45 14 13 17 19 0 0
0 0.000000 0.00000E+00
46 15 13 17 4 0 0
0 0.000000 0.00000E+00
47 15 13 17 18 0 0
0 0.000000 0.00000E+00
48 15 13 17 19 0 0
0 0.000000 0.00000E+00
49 4 17 19 20 0 0
0 0.000000 0.00000E+00
50 4 17 19 21 0 0
0 0.000000 0.00000E+00
51 4 17 19 23 0 0
0 0.000000 0.00000E+00
52 13 17 19 20 0 0
0 0.000000 0.00000E+00
53 13 17 19 21 0 0
0 0.000000 0.00000E+00
54 13 17 19 23 0 0
0 0.000000 0.00000E+00
55 18 17 19 20 0 0
0 0.000000 0.00000E+00
56 18 17 19 21 0 0
0 0.000000 0.00000E+00
57 18 17 19 23 0 0
0 0.000000 0.00000E+00
58 17 19 21 22 0 0
0 0.000000 0.00000E+00
59 20 19 21 22 0 0
0 0.000000 0.00000E+00
60 23 19 21 22 0 0
0 0.000000 0.00000E+00
61 17 19 23 24 0 0
0 0.000000 0.00000E+00
62 17 19 23 25 0 0
0 0.000000 0.00000E+00
63 17 19 23 26 0 0
0 0.000000 0.00000E+00
64 20 19 23 24 0 0
0 0.000000 0.00000E+00
65 20 19 23 25 0 0
0 0.000000 0.00000E+00
66 20 19 23 26 0 0
0 0.000000 0.00000E+00
67 21 19 23 24 0 0
0 0.000000 0.00000E+00
68 21 19 23 25 0 0
0 0.000000 0.00000E+00
69 21 19 23 26 0 0
0 0.000000 0.00000E+00
70 19 23 26 27 0 0
0 0.000000 0.00000E+00
71 24 23 26 27 0 0
0 0.000000 0.00000E+00
72 25 23 26 27 0 0
0 0.000000 0.00000E+00
1 5 3 1 2 0 0
0 0.000000 0.00000E+00

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
13 H5 H1 0 0 0 1 1 0.138770 0.000000
14 C6 CT 0 0 0 1 1 0.448428 0.000000
15 H6 H1 0 0 0 1 1 -0.088631 0.000000
16 OR OS 0 0 0 1 1 -0.653128 0.000000
17 C7 CT 0 0 0 1 1 0.387545 0.000000
18 H7 H1 0 0 0 1 1 -0.084796 0.000000
19 O7 OH 0 0 0 1 1 -0.757907 0.000000
20 HO7 HO 0 0 0 1 1 0.419274 0.000000
21 C8 CT 0 0 0 1 1 0.632846 0.000000
222H8 H1 0 0 0 1 1 -0.071639 0.000000
233H8 H1 0 0 0 1 1 -0.071639 0.000000
24 N8 N 0 0 0 1 1 -1.228155 0.000000
252HN8 H 0 0 0 1 1 0.434264 0.000000
263HN8 H 0 0 0 1 1 0.434264 0.000000
1 4 5 8 12 14 16 4
2 1 3
6 5 7
9 8 10 11
12 13
15 14 17 21 24
18 17 19 20
22 21 23
25 24 26

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
23 1 1 0
LCX
1 N N 1 1 0 1 1 -0.347900 0.000000
2 H2 H 0 0 0 1 1 0.274700 0.000000
3 CA CT 0 0 0 1 1 -0.498102 0.000000
4 HA H1 0 0 0 1 1 0.082916 0.000000
5 C C 2 1 0 1 1 0.734100 0.000000
6 O O 0 0 0 1 1 -0.589400 0.000000
7 CB CT 0 0 0 1 1 0.707723 0.000000
82HB HC 0 0 0 1 1 -0.197502 0.000000
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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
1 C1 AC 3 0 0 1 1 -0.162607 0.000000
2 H1 H2 0 0 0 1 1 0.182851 0.000000
3 C2 CT 0 0 0 1 1 -0.080535 0.000000
4 H2 H1 0 0 0 1 1 0.173175 0.000000
5 O2 OG 4 0 0 1 1 -0.079068 0.000000
6 C3 CT 0 0 0 1 1 0.020952 0.000000
7 H3 H1 0 0 0 1 1 0.156462 0.000000
8 C4 CT 0 0 0 1 1 0.277312 0.000000
9 H4 H1 0 0 0 1 1 0.055141 0.000000
10 O4 OH 0 0 0 1 1 -0.666790 0.000000
11 HO4 HO 0 0 0 1 1 0.440190 0.000000
12 C5 CT 0 0 0 1 1 -0.000761 0.000000
13 H5 H1 0 0 0 1 1 0.105583 0.000000
14 OR OS 0 0 0 1 1 -0.246681 0.000000
15 C6 CT 0 0 0 1 1 0.090569 0.000000
162H6 H1 0 0 0 1 1 0.071777 0.000000
173H6 H1 0 0 0 1 1 0.071777 0.000000
18 O6 OH 0 0 0 1 1 -0.573637 0.000000
19 HO6 HO 0 0 0 1 1 0.359359 0.000000
20 O3 OG 5 0 0 1 1 -0.195069 0.000000
1 2
1 3
1 14
3 4
3 5
3 6
6 7
6 8
6 20
8 9
8 10
8 12
10 11
12 13
12 14
12 15
15 16
15 17
15 18
18 19

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

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

@ -1,13 +0,0 @@
# N-terminal cap fragment
#
$NTR
6 1 1 0
NTR
1 C1 CT 0 0 0 1 1 -0.150000 0.000000
22H1 HC 0 0 0 1 1 0.050000 0.000000
33H1 HC 0 0 0 1 1 0.050000 0.000000
44H1 HC 0 0 0 1 1 0.050000 0.000000
5 C C 3 0 0 1 1 0.597300 0.000000
6 O O 0 0 0 1 1 -0.597300 0.000000
2 1 5 6
3 1 4

7
src/data/amber_q/Na.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
1Na 0 0 0 1 1
Na 1.000000 0.000000

14
src/data/amber_q/O4P.frg
View file

@ -1,14 +0,0 @@
# This is an automatically generated fragment file
#
$O4P
5 1 1 0
O4P
1 P P 3 0 0 1 1 1.222551 0.000000
2 OP1 OS 4 0 0 1 1 -0.275749 0.000000
3 OP2 O2 0 0 0 1 1 -0.818353 0.000000
4 OP3 O2 0 0 0 1 1 -0.818353 0.000000
5 OP4 OS 5 0 0 1 1 -0.310096 0.000000
1 2
1 3
1 4
1 5

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

@ -1,38 +0,0 @@
# This is an automatically generated fragment file
# Atom types and connectivity were derived from coordinates
# Atomic partial charges are crude guestimations
#
$PET
16 1 1 0
PET
1 C1 CT 3 0 0 1 1 -0.100000 0.000000
22H1 HC 0 0 0 1 1 0.050000 0.000000
33H1 HC 0 0 0 1 1 0.050000 0.000000
4 C2 CT 0 0 0 1 1 -0.100000 0.000000
52H2 HC 0 0 0 1 1 0.050000 0.000000
63H2 HC 0 0 0 1 1 0.050000 0.000000
7 C3 CT 0 0 0 1 1 -0.100000 0.000000
82H3 HC 0 0 0 1 1 0.050000 0.000000
93H3 HC 0 0 0 1 1 0.050000 0.000000
10 C4 CT 0 0 0 1 1 -0.100000 0.000000
112H4 HC 0 0 0 1 1 0.050000 0.000000
123H4 HC 0 0 0 1 1 0.050000 0.000000
13 C5 CT 0 0 0 1 1 -0.150000 0.000000
142H5 HC 0 0 0 1 1 0.050000 0.000000
153H5 HC 0 0 0 1 1 0.050000 0.000000
164H5 HC 0 0 0 1 1 0.050000 0.000000
1 2
1 3
1 4
4 5
4 6
4 7
7 8
7 9
7 10
10 11
10 12
10 13
13 14
13 15
13 16

187
src/data/amber_q/PET.sgm
View file

@ -1,187 +0,0 @@
# This is an automatically generated segment file
#
4.600000
16 15 27 33 0 0 1 1
0.000000
1 C1 3 0 0 1 1
CT -0.026814 0.000000
22H1 0 0 0 1 1
HC 0.013407 0.000000
33H1 0 0 0 1 1
HC 0.013407 0.000000
4 C2 0 0 0 1 1
CT -0.100000 0.000000
52H2 0 0 0 1 1
HC 0.050000 0.000000
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src/data/amber_q/PNT.frg
View file

@ -1,34 +0,0 @@
# This is an automatically generated fragment file
#
$PNT
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14
src/data/amber_q/PO4.frg
View file

@ -1,14 +0,0 @@
# This is an automatically generated fragment file
#
$PO4
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35
src/data/amber_q/PO4.sgm
View file

@ -1,35 +0,0 @@
# This is an automatically generated segment file
#
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src/data/amber_q/PPO.frg
View file

@ -1,22 +0,0 @@
# This is an automatically generated fragment file
#
$PPO
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47
src/data/amber_q/RH2.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
#
$RH2
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263
src/data/amber_q/RH2.sgm
View file

@ -1,263 +0,0 @@
# This is an automatically generated segment file
#
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src/data/amber_q/RH3.sgm
View file

@ -1,263 +0,0 @@
# This is an automatically generated segment file
#
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26 4 8 11 15 0 0
0 0.000000 0.00000E+00
27 9 8 11 12 0 0
0 0.000000 0.00000E+00
28 9 8 11 13 0 0
0 0.000000 0.00000E+00
29 9 8 11 15 0 0
0 0.000000 0.00000E+00
30 10 8 11 12 0 0
0 0.000000 0.00000E+00
31 10 8 11 13 0 0
0 0.000000 0.00000E+00
32 10 8 11 15 0 0
0 0.000000 0.00000E+00
33 8 11 13 14 0 0
0 0.000000 0.00000E+00
34 12 11 13 14 0 0
0 0.000000 0.00000E+00
35 15 11 13 14 0 0
0 0.000000 0.00000E+00
36 8 11 15 3 0 0
0 0.000000 0.00000E+00
37 8 11 15 16 0 0
0 0.000000 0.00000E+00
38 8 11 15 17 0 0
0 0.000000 0.00000E+00
39 12 11 15 3 0 0
0 0.000000 0.00000E+00
40 12 11 15 16 0 0
0 0.000000 0.00000E+00
41 12 11 15 17 0 0
0 0.000000 0.00000E+00
42 13 11 15 3 0 0
0 0.000000 0.00000E+00
43 13 11 15 16 0 0
0 0.000000 0.00000E+00
44 13 11 15 17 0 0
0 0.000000 0.00000E+00
45 3 15 17 18 0 0
0 0.000000 0.00000E+00
46 3 15 17 19 0 0
0 0.000000 0.00000E+00
47 3 15 17 20 0 0
0 0.000000 0.00000E+00
48 11 15 17 18 0 0
0 0.000000 0.00000E+00
49 11 15 17 19 0 0
0 0.000000 0.00000E+00
50 11 15 17 20 0 0
0 0.000000 0.00000E+00
51 16 15 17 18 0 0
0 0.000000 0.00000E+00
52 16 15 17 19 0 0
0 0.000000 0.00000E+00
53 16 15 17 20 0 0
0 0.000000 0.00000E+00

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

@ -1,45 +0,0 @@
# This is an automatically generated fragment file
#
$RHA
20 1 1 0
RHA
1 C1 AC 3 0 0 1 1 -0.362918 0.000000
2 H1 H2 0 0 0 1 1 0.338065 0.000000
3 C2 CT 0 0 0 1 1 0.081671 0.000000
4 H2 H1 0 0 0 1 1 0.117337 0.000000
5 O2 OH 0 0 0 1 1 -0.580083 0.000000
6 HO2 HO 0 0 0 1 1 0.420095 0.000000
7 C3 CT 0 0 0 1 1 0.055135 0.000000
8 H3 H1 0 0 0 1 1 0.089139 0.000000
9 O3 OH 0 0 0 1 1 -0.613470 0.000000
10 HO3 HO 0 0 0 1 1 0.429006 0.000000
11 C4 CT 0 0 0 1 1 0.090177 0.000000
12 H4 H1 0 0 0 1 1 0.199352 0.000000
13 O4 OG 4 0 0 1 1 -0.206307 0.000000
14 C5 CT 0 0 0 1 1 0.091230 0.000000
15 H5 H1 0 0 0 1 1 0.074855 0.000000
16 OR OS 0 0 0 1 1 -0.233814 0.000000
17 C6 CT 0 0 0 1 1 -0.204654 0.000000
182H6 HC 0 0 0 1 1 0.071728 0.000000
193H6 HC 0 0 0 1 1 0.071728 0.000000
204H6 HC 0 0 0 1 1 0.071728 0.000000
1 2
1 3
1 16
3 4
3 5
3 7
5 6
7 8
7 9
7 11
9 10
11 12
11 13
11 14
14 15
14 16
14 17
17 18
17 19
17 20

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

@ -1,30 +0,0 @@
$SEP
14 1 1 0
SEP
1 N N 1 1 0 1 1 -0.415700 0.000000
2 H H 0 0 0 1 1 0.271900 0.000000
3 CA CT 0 0 0 1 1 -0.824145 0.000000
4 HA H1 0 0 0 1 1 0.402169 0.000000
5 CB CT 0 0 0 1 1 1.255182 0.000000
62HB H1 0 0 0 1 1 -0.181987 0.000000
73HB H1 0 0 0 1 1 -0.252644 0.000000
8 OG OS 0 0 0 1 1 -0.906468 0.000000
9 C C 2 1 0 1 1 0.597300 0.000000
10 O O 0 0 0 1 1 -0.567900 0.000000
11 P P 0 0 0 1 1 1.848480 0.000000
12 O1P O2 0 0 0 1 1 -1.082268 0.000000
13 O2P O2 0 0 0 1 1 -1.078626 0.000000
14 O3P O2 0 0 0 1 1 -1.065292 0.000000
1 2
1 3
3 9
3 4
3 5
5 8
5 6
5 7
8 11
9 10
11 14
11 12
11 13

16
src/data/amber_q/SO4.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
#
$SO4
5 1 1 0
SO4
1 S S 0 0 0 1 1 0.000000 0.000000
2 O1 O2 0 0 0 1 1 -0.500000 0.000000
3 O2 O2 0 0 0 1 1 -0.500000 0.000000
4 O3 O2 0 0 0 1 1 -0.500000 0.000000
5 O4 O2 0 0 0 1 1 -0.500000 0.000000
1 2
1 3
1 4
1 5

41
src/data/amber_q/TPO.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 estimates
# 11/08/04 18:38:58
#
$TPO
17 1 1 0
TPO
1 N N 1 1 0 1 1 -0.415700 0.000000
2 H H 0 0 0 1 1 0.271900 0.000000
3 CA CT 0 0 0 1 1 -0.639337 0.000000
4 HA H1 0 0 0 1 1 0.123871 0.000000
5 CB CT 0 0 0 1 1 1.565340 0.000000
6 HB H1 0 0 0 1 1 -0.209754 0.000000
7 CG2 CT 0 0 0 1 1 -0.680243 0.000000
82HG2 HC 0 0 0 1 1 0.057615 0.000000
93HG2 HC 0 0 0 1 1 0.044406 0.000000
104HG2 HC 0 0 0 1 1 0.137305 0.000000
11 OG1 OS 0 0 0 1 1 -0.897338 0.000000
12 C C 2 1 0 1 1 0.597300 0.000000
13 O O 0 0 0 1 1 -0.567900 0.000000
14 O3 O2 0 0 0 1 1 -1.112264 0.000000
15 O2 O2 0 0 0 1 1 -1.025128 0.000000
16 O1 O2 0 0 0 1 1 -1.089571 0.000000
17 P P 0 0 0 1 1 1.839497 0.000000
1 2
1 3
3 4
3 5
3 12
5 6
5 7
5 11
7 8
7 9
7 10
11 17
12 13
14 17
15 17
16 17

219
src/data/amber_q/amber.par
View file

@ -1,219 +0,0 @@
This is the AMBER96 user defined parameter file for NWChem 3.2 and ARGOS 7.0
Electrostatic 1-4 scaling factor 0.833333
Relative dielectric constant 1.000000
Parameters epsilon R*
Atoms
Ne 20.17900 3.16779E-01 1.55006E-01 1 1111111111
10 1.58389E-01 1.55006E-01 TPS000106 JCP 85, 6720-6727 (1986)
Mg 24.30500 4.30952E-02 1.36000E-01 1 1111111111
12 2.15476E-02 1.36000E-01 TPS000106 JCC 12, 1125-1128 (1991)
Ca 40.08000 3.78520E-02 1.74000E-01 1 1111111111
20 1.89260E-02 1.74000E-01 TPS000106 JCC 12, 1125-1128 (1991)
Sr 87.62000 2.70286E-01 1.92000E-01 1 1111111111
38 1.35143E-01 1.92000E-01 TPS000106 JCC 12, 1125-1128 (1991)
Cl 35.45300 4.44950E-01 2.50000E-01 1 1111111111
17 2.22475E-01 2.50000E-01
CD 12.01100 3.59820E-01 1.90800E-01 1 1111111111
6 1.79910E-01 1.90800E-01
CY 12.01100 3.59820E-01 1.90800E-01 1 1111111111
6 1.79910E-01 1.90800E-01
CX 12.01100 3.59820E-01 1.90800E-01 1 1111111111
6 1.79910E-01 1.90800E-01
NO 14.00674 7.11283E-01 1.82400E-01 1 1111111111
7 3.55641E-01 1.82400E-01
NP 14.00674 7.11283E-01 1.82400E-01 1 1111111111
7 3.55641E-01 1.82400E-01
Cross
Bonds
FE -NO 0.20100 4.18400E+04
FE -NP 0.20100 4.18400E+04
CC -NP 0.13840 2.64429E+05
CB -CC 0.14440 2.28446E+05
CC -CD 0.13910 3.27189E+05
CB -CT 0.15010 2.48530E+05
HC -CD 0.10900 2.82838E+05
CC -NO 0.13840 2.64429E+05
CB -CY 0.15010 2.48530E+05
HC -CY 0.10900 2.84512E+05
CX -CY 0.13400 4.76976E+05
HC -CX 0.10900 2.84512E+05
AC -H2 0.10900 2.84512E+05 tps990729 copy CT-H2
EC -H2 0.10900 2.84512E+05 tps990729 copy CT-H2
C -OS 0.14100 2.67776E+05 tps990729 copy CT-OS
C -AC 0.15220 2.65266E+05 tps990729 copy C-CT
S -O2 0.14900 1.69566E+05 tps991219 for SO4-- taken from Smith
Angles
C -CT -OH 1.91114 4.18400E+02
CB -CB -CC 1.86750 5.85760E+02
CB -CB -CT 2.23751 5.85760E+02
CB -CB -CY 2.23751 5.85760E+02
CB -CC -CD 2.18864 5.85760E+02
CB -CC -NO 1.92510 5.85760E+02
CB -CC -NP 1.92510 5.85760E+02
CD -CC -NO 2.19039 5.85760E+02
CD -CC -NP 2.19039 5.85760E+02
CC -CB -CT 2.17992 5.85760E+02
CC -CB -CY 2.17992 5.85760E+02
HC -CD -CC 2.05949 2.51040E+02
CC -CD -CC 2.16595 5.85760E+02
HC -CT -CB 1.91114 2.92880E+02
CB -CT -CT 1.98968 5.27184E+02
CT -CT -Cl 1.91986 3.55810E+02
Cl -CT -Cl 1.94604 4.18600E+02
HC -CX -HC 2.09440 2.92880E+02
HC -CX -CY 2.09440 2.92880E+02
HC -CY -CB 2.09440 2.92880E+02
HC -CY -CX 2.09440 2.92880E+02
CB -CY -CX 2.09440 5.85760E+02
CC -NO -CC 1.83958 5.85760E+02
CC -NO -FE 2.22355 2.51040E+02
CC -NP -CC 1.83958 5.85760E+02
CC -NP -FE 2.22355 2.51040E+02
NB -FE -NO 1.57080 4.18400E+02
NB -FE -NP 1.57080 4.18400E+02
NO -FE -NO 1.57080 0.00000E+00
NO -FE -NP 1.57080 4.18400E+02
NP -FE -NP 1.57080 0.00000E+00
N2 -CA -CT 2.09440 5.85760E+02 rdl000731 taken from N2-CA-N2
CM -C -O2 2.04204 5.85760E+02 tps020326 taken from CT-C-O2
CB -CT -S 2.00189 4.18400E+02 tps020326 taken from CT-CT-S
CB -CT -H1 1.91114 4.18400E+02 tps020326 taken from CM-CT-H1
H2 -AC -OS 1.91114 4.18400E+02 tps990729 copy H2-CT-OS
H2 -AC -OG 1.91114 4.18400E+02 tps990729 copy H2-CT-OS
H2 -EC -OG 1.91114 4.18400E+02 tps000315 copy H2-CT-OS
H2 -EC -OS 1.91114 4.18400E+02 tps980817
OS -AC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-OS
OS -EC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-H2
CT -AC -H2 1.91114 4.18400E+02 tps980817
CT -EC -H2 1.91114 4.18400E+02 tps980817
AC -CT -H1 1.91114 4.18400E+02 tps990729 copy CT-CT-H1
EC -CT -H1 1.91114 4.18400E+02 tps980817
AC -CT -N 1.91114 4.18400E+02 tps990729 copy CT-CT-N*
EC -CT -N 1.91114 4.18400E+02 tps980817
CT -OS -C 1.91114 5.02080E+02 tps990729 copy CT-OS-CT
H1 -CT -OG 1.91114 4.18400E+02 tps990729 copy H1-CT-OS
CT -OG -CT 1.91114 5.02080E+02 tps990729 copy CT-OS-CT
AC -OS -P 2.10312 8.36800E+02 tps980817 copy CT-OS-P
EC -OS -P 2.10312 8.36800E+02 tps980817
OS -C -O 2.19911 6.69440E+02 tps980817
CT -C -OS 2.04204 5.85760E+02 tps980817
AC -C -O 2.10138 6.69440E+02 tps990729 copy CT-C-O
AC -C -OH 2.04204 5.85760E+02 tps990729 copy CT-C-OH
C -AC -OG 1.91114 4.18400E+02 tps990729 copy CT-CT-OS
C -AC -OS 1.91114 4.18400E+02 tps990729 copy CT-CT-OS
C -AC -CT 1.93906 5.27184E+02 tps990729 copy C-CT-CT
OG -CT -C 1.91114 4.18400E+02 tps990729 copy OS-CT-CT
OS -CT -C 1.91114 4.18400E+02 tps990729 copy OS-CT-CT
OG -CT -OS 1.91114 4.18400E+02 tps990729 copy N*-CT-OS
AC -C -O2 2.04204 5.85760E+02 tps990729 copy CT-C-O2
OS -C -O2 2.19911 6.69440E+02 tps990729 copy O2-C-O2
Proper dihedrals
-NB -FE - 0.00000 0.00000E+02 2
-NO -FE - 3.14159 0.00000E+02 2
-NP -FE - 3.14159 0.00000E+02 2
-CB -CC - 3.14159 3.29490E+00 2
-CB -CT - 3.14159 0.00000E+00 2
-CB -CY - 3.14159 0.00000E+00 2
-CC -CD - 3.14159 8.26340E+00 2
-CC -NO - 3.14159 5.96220E+00 2
-CC -NP - 3.14159 5.96220E+00 2
-CX -CY - 3.14159 3.13800E+01 2
-C -OS - 3.14159 6.06680E+00 2 tps990729 copy -C-N*-
-AC -OG - 0.00000 1.60387E+00 3 tps990729 copy -CT-OS-
-EC -OG - 0.00000 1.60387E+00 3 tps000315 copy -CT-OS-
C -AC -OG -CT 0.52360 1.58992E+00 -3 tps990729 copy CT-CT-OS-CT
C -AC -OG -CT 3.14159 4.18400E-01 2 tps990729 copy CT-CT-OS-CT
-C -AC - 0.00000 0.00000E+00 2 tps990729 copy -C-CT-
CT -EC -N -H 0.00000 0.00000E+00 1
CT -EC -OH -HO 0.00000 6.97333E-01 3
Improper dihedrals
- -CC -CC 3.14159 4.18400E+00 2
- -CC -CB 3.14159 4.18400E+00 2
- -CB -NP 3.14159 4.18400E+00 2
- -CB -NO 3.14159 4.18400E+00 2
- -CB -CY 3.14159 4.18400E+00 2
- -CB -CT 3.14159 4.18400E+00 2
- -CD -HC 3.14159 4.18400E+00 2
- -N* -H 3.14159 4.50240E+00 2
Atom types
Li 3 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
Na 11 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
Mg 12 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
K 19 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
Ca 20 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
Rb 37 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
Sr 38 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
Cl 17 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
O2 8 0 0 0 1 15 4 808 1808 800
0 0 0 0 0
0 0 0 0 0
#
O2 8 0 0 0 1 15 4 0 0 0
0 0 0 0 0
0 0 0 0 0
#
N 7 0 0 0 3 1 0 0 0 0
15 4 0 0 0
15 4 0 0 0
#
N3 7 0 0 0 3 6 4 0 0 0
6 4 0 0 0
6 4 0 0 0
O2 8 0 0 0 1 16 0 0 0 0
0 0 0 0 0
0 0 0 0 0
S 16 0 0 0 4 8 0 0 0 0
8 0 0 0 0
8 0 0 0 0
NB 7 0 0 0 3 1 0 0 0 0
6 3 7 1 0
6 3 6 6 0
#
CB 6 0 0 66 3 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
N3 7 0 0 0 4 6 0 0 0 0
6 0 0 0 0
6 0 0 0 0
N 7 0 0 0 3 6 4 6 6 1
6 4 6 6 1
1 1 0 0 0
#
# cation definitions
#
#
CL 17 0 0 0 1 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#
#OG 8 0 0 0 2 6 4 0 0 0
# 6 4 0 0 0
# 0 0 0 0 0
End
#

14
src/data/amber_q/coc.frg
View file

@ -1,14 +0,0 @@
# Fragment definition for crown ether fragment -CH2-O-CH2-
$coc
7 1 1 0
coc
1 C1 CT 3 0 0 1 1 0.000000 0.000000
22H1 H1 0 0 0 1 1 0.150000 0.000000
33H1 H1 0 0 0 1 1 0.150000 0.000000
4 O OS 0 0 0 1 1 -0.600000 0.000000
5 C2 CT 4 0 0 1 1 0.000000 0.000000
62H2 H1 0 0 0 1 1 0.150000 0.000000
73H2 H1 0 0 0 1 1 0.150000 0.000000
1 4 5
2 1 3
6 5 7

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