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Commit 52042c41 authored by peastman's avatar peastman
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Merge pull request #922 from swails/gmxdefines 

Fix Gromacs #define replacement and add support for Gromacs 5
parents 78e8a786 3e84be61
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Showing with 1638 additions and 5 deletions
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 52042c41
......@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2015 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Contributors: Jason Swails
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -40,7 +40,9 @@ import simtk.unit as unit
import simtk.openmm as mm
import math
import os
import re
import distutils.spawn
from collections import OrderedDict
HBonds = ff.HBonds
AllBonds = ff.AllBonds
......@@ -48,6 +50,57 @@ HAngles = ff.HAngles
OBC2 = prmtop.OBC2
novarcharre = re.compile(r'\W')
def _find_all_instances_in_string(string, substr):
""" Find indices of all instances of substr in string """
indices = []
idx = string.find(substr, 0)
while idx > -1:
indices.append(idx)
idx = string.find(substr, idx+1)
return indices
def _replace_defines(line, defines):
""" Replaces defined tokens in a given line """
if not defines: return line
for define in reversed(defines):
value = defines[define]
indices = _find_all_instances_in_string(line, define)
if not indices: continue
# Check to see if it's inside of quotes
inside = ''
idx = 0
n_to_skip = 0
new_line = []
for i, char in enumerate(line):
if n_to_skip:
n_to_skip -= 1
continue
if char in ('\'"'):
if not inside:
inside = char
else:
if inside == char:
inside = ''
if idx < len(indices) and i == indices[idx]:
if inside:
new_line.append(char)
idx += 1
continue
if i == 0 or novarcharre.match(line[i-1]):
endidx = indices[idx] + len(define)
if endidx >= len(line) or novarcharre.match(line[endidx]):
new_line.extend(list(value))
n_to_skip = len(define) - 1
idx += 1
continue
idx += 1
new_line.append(char)
line = ''.join(new_line)
return line
class GromacsTopFile(object):
"""GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it."""
......@@ -113,6 +166,7 @@ class GromacsTopFile(object):
name = fields[1]
valueStart = stripped.find(name, len(command))+len(name)+1
value = line[valueStart:].strip()
value = value or '1' # Default define is 1
self._defines[name] = value
elif command == '#ifdef':
# See whether this block should be ignored.
......@@ -121,6 +175,12 @@ class GromacsTopFile(object):
name = fields[1]
self._ifStack.append(name in self._defines)
self._elseStack.append(False)
elif command == '#undef':
# Un-define a variable
if len(fields) < 2:
raise ValueError('Illegal line in .top file: '+line)
if fields[1] in self._defines:
self._defines.pop(fields[1])
elif command == '#ifndef':
# See whether this block should be ignored.
if len(fields) < 2:
......@@ -145,6 +205,11 @@ class GromacsTopFile(object):
self._elseStack[-1] = True
elif not ignore:
# Gromacs occasionally uses #define's to introduce specific
# parameters for individual terms (for instance, this is how
# ff99SB-ILDN is implemented). So make sure we do the appropriate
# pre-processor replacements necessary
line = _replace_defines(line, self._defines)
# A line of data for the current category
if self._currentCategory is None:
raise ValueError('Unexpected line in .top file: '+line)
......@@ -379,9 +444,11 @@ class GromacsTopFile(object):
# unless the preprocessor #define FLEXIBLE is given, don't define
# bonds between the water hydrogen and oxygens, but only give the
# constraint distances and exclusions.
self._defines = {'FLEXIBLE': True}
self._defines = OrderedDict()
self._defines['FLEXIBLE'] = True
if defines is not None:
self._defines.update(defines)
for define, value in defines.iteritems():
self._defines[define] = value
# Parse the file.
......@@ -796,8 +863,8 @@ class GromacsTopFile(object):
def _defaultGromacsIncludeDir():
"""Find the location where gromacs #include files are referenced from, by
searching for (1) gromacs environment variables, (2) for the gromacs binary
'pdb2gmx' in the PATH, or (3) just using the default gromacs install
location, /usr/local/gromacs/share/gromacs/top """
'pdb2gmx' or 'gmx' in the PATH, or (3) just using the default gromacs
install location, /usr/local/gromacs/share/gromacs/top """
if 'GMXDATA' in os.environ:
return os.path.join(os.environ['GMXDATA'], 'top')
if 'GMXBIN' in os.environ:
......@@ -806,5 +873,9 @@ def _defaultGromacsIncludeDir():
pdb2gmx_path = distutils.spawn.find_executable('pdb2gmx')
if pdb2gmx_path is not None:
return os.path.abspath(os.path.join(os.path.dirname(pdb2gmx_path), '..', 'share', 'gromacs', 'top'))
else:
gmx_path = distutils.spawn.find_executable('gmx')
if gmx_path is not None:
return os.path.abspath(os.path.join(os.path.dirname(gmx_path), '..', 'share', 'gromacs', 'top'))
return '/usr/local/gromacs/share/gromacs/top'
wrappers/python/tests/TestGromacsTopFile.py
View file @ 52042c41
......@@ -31,6 +31,20 @@ class TestGromacsTopFile(unittest.TestCase):
f.getNonbondedMethod()==methodMap[method]
for f in forces))
def test_ff99SBILDN(self):
""" Test Gromacs topology #define replacement as used in ff99SB-ILDN """
top = GromacsTopFile('systems/aidilnaaaaa.top')
gro = GromacsGroFile('systems/aidilnaaaaa.gro')
system = top.createSystem()
for force in system.getForces():
if isinstance(force, PeriodicTorsionForce):
force.setForceGroup(1)
context = Context(system, VerletIntegrator(1*femtosecond),
Platform.getPlatformByName('Reference'))
context.setPositions(gro.positions)
ene = context.getState(getEnergy=True, groups=2**1).getPotentialEnergy()
self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 341.6905133582857)
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
......
wrappers/python/tests/systems/aidilnaaaaa.gro 0 → 100644
View file @ 52042c41
S C A M O R G
146
1ALA N 1 0.333 0.155 -0.000
1ALA H1 2 0.360 0.104 -0.082
1ALA H2 3 0.360 0.104 0.082
1ALA H3 4 0.233 0.167 0.000
1ALA CA 5 0.397 0.285 -0.000
1ALA HA 6 0.364 0.328 -0.084
1ALA CB 7 0.358 0.365 0.123
1ALA HB1 8 0.403 0.454 0.121
1ALA HB2 9 0.259 0.379 0.124
1ALA HB3 10 0.385 0.316 0.206
1ALA C 11 0.549 0.271 -0.000
1ALA O 12 0.601 0.159 -0.000
2ILE N 13 0.619 0.384 -0.000
2ILE H 14 0.571 0.471 0.000
2ILE CA 15 0.764 0.384 -0.000
2ILE HA 16 0.791 0.337 0.084
2ILE CB 17 0.815 0.312 -0.124
2ILE HB 18 0.781 0.218 -0.124
2ILE CG2 19 0.764 0.384 -0.249
2ILE HG21 20 0.797 0.337 -0.331
2ILE HG22 21 0.664 0.384 -0.249
2ILE HG23 22 0.797 0.478 -0.249
2ILE CG1 23 0.967 0.312 -0.124
2ILE HG11 24 1.001 0.265 -0.043
2ILE HG12 25 1.001 0.406 -0.125
2ILE CD 26 1.018 0.240 -0.249
2ILE HD1 27 1.118 0.240 -0.249
2ILE HD2 28 0.985 0.146 -0.249
2ILE HD3 29 0.985 0.287 -0.331
2ILE C 30 0.819 0.526 -0.000
2ILE O 31 0.743 0.622 0.000
3ASP N 32 0.952 0.539 -0.000
3ASP H 33 1.008 0.456 0.000
3ASP CA 34 1.016 0.668 0.000
3ASP HA 35 0.983 0.711 -0.084
3ASP CB 36 0.977 0.749 0.123
3ASP HB1 37 1.004 0.700 0.206
3ASP HB2 38 0.878 0.763 0.124
3ASP CG 39 1.047 0.885 0.119
3ASP OD1 40 0.986 0.979 0.062
3ASP OD2 41 1.160 0.893 0.174
3ASP C 42 1.168 0.654 -0.000
3ASP O 43 1.220 0.543 -0.000
4ILE N 44 1.238 0.768 -0.000
4ILE H 45 1.190 0.855 0.000
4ILE CA 46 1.383 0.768 -0.000
4ILE HA 47 1.410 0.720 0.084
4ILE CB 48 1.434 0.696 -0.124
4ILE HB 49 1.401 0.602 -0.124
4ILE CG2 50 1.383 0.768 -0.249
4ILE HG21 51 1.416 0.721 -0.331
4ILE HG22 52 1.283 0.768 -0.249
4ILE HG23 53 1.416 0.862 -0.249
4ILE CG1 54 1.586 0.696 -0.124
4ILE HG11 55 1.620 0.649 -0.043
4ILE HG12 56 1.620 0.790 -0.125
4ILE CD 57 1.637 0.624 -0.249
4ILE HD1 58 1.737 0.624 -0.249
4ILE HD2 59 1.604 0.530 -0.249
4ILE HD3 60 1.604 0.671 -0.331
4ILE C 61 1.438 0.910 -0.000
4ILE O 62 1.362 1.006 0.000
5LEU N 63 1.571 0.923 -0.000
5LEU H 64 1.628 0.840 0.000
5LEU CA 65 1.635 1.052 0.000
5LEU HA 66 1.602 1.095 -0.084
5LEU CB 67 1.596 1.133 0.123
5LEU HB1 68 1.623 1.084 0.206
5LEU HB2 69 1.497 1.147 0.124
5LEU CG 70 1.666 1.269 0.119
5LEU HG 71 1.765 1.255 0.119
5LEU CD1 72 1.623 1.344 -0.006
5LEU HD11 73 1.669 1.433 -0.009
5LEU HD12 74 1.649 1.291 -0.087
5LEU HD13 75 1.524 1.357 -0.006
5LEU CD2 76 1.626 1.349 0.243
5LEU HD21 77 1.672 1.438 0.240
5LEU HD22 78 1.527 1.363 0.244
5LEU HD23 79 1.654 1.300 0.325
5LEU C 80 1.787 1.038 -0.000
5LEU O 81 1.839 0.927 -0.000
6ASN N 82 1.857 1.152 -0.000
6ASN H 83 1.809 1.239 0.000
6ASN CA 84 2.002 1.152 -0.000
6ASN HA 85 2.026 1.103 0.084
6ASN CB 86 2.057 1.080 -0.123
6ASN HB1 87 2.025 1.127 -0.205
6ASN HB2 88 2.025 0.986 -0.124
6ASN CG 89 2.209 1.080 -0.123
6ASN OD1 90 2.272 1.133 -0.032
6ASN ND2 91 2.269 1.021 -0.227
6ASN HD21 92 2.214 0.979 -0.299
6ASN HD22 93 2.369 1.018 -0.232
6ASN C 94 2.057 1.294 -0.000
6ASN O 95 1.981 1.390 0.000
7ALA N 96 2.190 1.306 -0.000
7ALA H 97 2.247 1.224 0.000
7ALA CA 98 2.254 1.436 0.000
7ALA HA 99 2.222 1.479 -0.084
7ALA CB 100 2.215 1.517 0.123
7ALA HB1 101 2.261 1.606 0.121
7ALA HB2 102 2.116 1.530 0.124
7ALA HB3 103 2.243 1.468 0.206
7ALA C 104 2.406 1.422 -0.000
7ALA O 105 2.458 1.311 -0.000
8ALA N 106 2.476 1.535 -0.000
8ALA H 107 2.428 1.623 0.000
8ALA CA 108 2.621 1.535 -0.000
8ALA HA 109 2.645 1.487 0.084
8ALA CB 110 2.676 1.464 -0.123
8ALA HB1 111 2.776 1.466 -0.121
8ALA HB2 112 2.644 1.370 -0.124
8ALA HB3 113 2.644 1.511 -0.206
8ALA C 114 2.676 1.677 0.000
8ALA O 115 2.600 1.774 0.000
9ALA N 116 2.809 1.690 -0.000
9ALA H 117 2.866 1.608 -0.000
9ALA CA 118 2.873 1.820 0.000
9ALA HA 119 2.841 1.863 -0.084
9ALA CB 120 2.834 1.901 0.123
9ALA HB1 121 2.880 1.990 0.121
9ALA HB2 122 2.735 1.914 0.124
9ALA HB3 123 2.862 1.851 0.206
9ALA C 124 3.025 1.806 -0.000
9ALA O 125 3.077 1.695 -0.000
10ALA N 126 3.095 1.919 -0.000
10ALA H 127 3.047 2.007 0.000
10ALA CA 128 3.240 1.919 -0.000
10ALA HA 129 3.264 1.871 0.084
10ALA CB 130 3.295 1.848 -0.123
10ALA HB1 131 3.395 1.850 -0.121
10ALA HB2 132 3.263 1.753 -0.124
10ALA HB3 133 3.263 1.895 -0.206
10ALA C 134 3.295 2.061 0.000
10ALA O 135 3.219 2.158 0.000
11ALA N 136 3.428 2.074 -0.000
11ALA H 137 3.485 1.992 -0.000
11ALA CA 138 3.493 2.204 0.000
11ALA HA 139 3.460 2.247 -0.084
11ALA CB 140 3.453 2.285 0.123
11ALA HB1 141 3.499 2.374 0.121
11ALA HB2 142 3.354 2.298 0.124
11ALA HB3 143 3.481 2.235 0.206
11ALA C 144 3.644 2.190 -0.000
11ALA OC1 145 3.716 2.289 -0.000
11ALA OC2 146 3.696 2.079 -0.000
3.48257 2.26962 0.65582
wrappers/python/tests/systems/aidilnaaaaa.top 0 → 100644
View file @ 52042c41
;
; File 'topol.top' was generated
; By user: swails (44411)
; On host: batman
; At date: Mon May 18 10:00:34 2015
;
; This is a standalone topology file
;
; Created by:
; GROMACS: gmx pdb2gmx, VERSION 5.0.4
; Executable: /usr/bin/gmx
; Library dir: /usr/share/gromacs/top
; Command line:
; gmx pdb2gmx -f AIDILNAAAAA.pdb -ff amber99sb-ildn -ignh
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ALA rtp NALA q +1.0
1 N3 1 ALA N 1 0.1414 14.01 ; qtot 0.1414
2 H 1 ALA H1 2 0.1997 1.008 ; qtot 0.3411
3 H 1 ALA H2 3 0.1997 1.008 ; qtot 0.5408
4 H 1 ALA H3 4 0.1997 1.008 ; qtot 0.7405
5 CT 1 ALA CA 5 0.0962 12.01 ; qtot 0.8367
6 HP 1 ALA HA 6 0.0889 1.008 ; qtot 0.9256
7 CT 1 ALA CB 7 -0.0597 12.01 ; qtot 0.8659
8 HC 1 ALA HB1 8 0.03 1.008 ; qtot 0.8959
9 HC 1 ALA HB2 9 0.03 1.008 ; qtot 0.9259
10 HC 1 ALA HB3 10 0.03 1.008 ; qtot 0.9559
11 C 1 ALA C 11 0.6163 12.01 ; qtot 1.572
12 O 1 ALA O 12 -0.5722 16 ; qtot 1
; residue 2 ILE rtp ILE q 0.0
13 N 2 ILE N 13 -0.4157 14.01 ; qtot 0.5843
14 H 2 ILE H 14 0.2719 1.008 ; qtot 0.8562
15 CT 2 ILE CA 15 -0.0597 12.01 ; qtot 0.7965
16 H1 2 ILE HA 16 0.0869 1.008 ; qtot 0.8834
17 CT 2 ILE CB 17 0.1303 12.01 ; qtot 1.014
18 HC 2 ILE HB 18 0.0187 1.008 ; qtot 1.032
19 CT 2 ILE CG2 19 -0.3204 12.01 ; qtot 0.712
20 HC 2 ILE HG21 20 0.0882 1.008 ; qtot 0.8002
21 HC 2 ILE HG22 21 0.0882 1.008 ; qtot 0.8884
22 HC 2 ILE HG23 22 0.0882 1.008 ; qtot 0.9766
23 CT 2 ILE CG1 23 -0.043 12.01 ; qtot 0.9336
24 HC 2 ILE HG11 24 0.0236 1.008 ; qtot 0.9572
25 HC 2 ILE HG12 25 0.0236 1.008 ; qtot 0.9808
26 CT 2 ILE CD 26 -0.066 12.01 ; qtot 0.9148
27 HC 2 ILE HD1 27 0.0186 1.008 ; qtot 0.9334
28 HC 2 ILE HD2 28 0.0186 1.008 ; qtot 0.952
29 HC 2 ILE HD3 29 0.0186 1.008 ; qtot 0.9706
30 C 2 ILE C 30 0.5973 12.01 ; qtot 1.568
31 O 2 ILE O 31 -0.5679 16 ; qtot 1
; residue 3 ASP rtp ASP q -1.0
32 N 3 ASP N 32 -0.5163 14.01 ; qtot 0.4837
33 H 3 ASP H 33 0.2936 1.008 ; qtot 0.7773
34 CT 3 ASP CA 34 0.0381 12.01 ; qtot 0.8154
35 H1 3 ASP HA 35 0.088 1.008 ; qtot 0.9034
36 CT 3 ASP CB 36 -0.0303 12.01 ; qtot 0.8731
37 HC 3 ASP HB1 37 -0.0122 1.008 ; qtot 0.8609
38 HC 3 ASP HB2 38 -0.0122 1.008 ; qtot 0.8487
39 C 3 ASP CG 39 0.7994 12.01 ; qtot 1.648
40 O2 3 ASP OD1 40 -0.8014 16 ; qtot 0.8467
41 O2 3 ASP OD2 41 -0.8014 16 ; qtot 0.0453
42 C 3 ASP C 42 0.5366 12.01 ; qtot 0.5819
43 O 3 ASP O 43 -0.5819 16 ; qtot 0
; residue 4 ILE rtp ILE q 0.0
44 N 4 ILE N 44 -0.4157 14.01 ; qtot -0.4157
45 H 4 ILE H 45 0.2719 1.008 ; qtot -0.1438
46 CT 4 ILE CA 46 -0.0597 12.01 ; qtot -0.2035
47 H1 4 ILE HA 47 0.0869 1.008 ; qtot -0.1166
48 CT 4 ILE CB 48 0.1303 12.01 ; qtot 0.0137
49 HC 4 ILE HB 49 0.0187 1.008 ; qtot 0.0324
50 CT 4 ILE CG2 50 -0.3204 12.01 ; qtot -0.288
51 HC 4 ILE HG21 51 0.0882 1.008 ; qtot -0.1998
52 HC 4 ILE HG22 52 0.0882 1.008 ; qtot -0.1116
53 HC 4 ILE HG23 53 0.0882 1.008 ; qtot -0.0234
54 CT 4 ILE CG1 54 -0.043 12.01 ; qtot -0.0664
55 HC 4 ILE HG11 55 0.0236 1.008 ; qtot -0.0428
56 HC 4 ILE HG12 56 0.0236 1.008 ; qtot -0.0192
57 CT 4 ILE CD 57 -0.066 12.01 ; qtot -0.0852
58 HC 4 ILE HD1 58 0.0186 1.008 ; qtot -0.0666
59 HC 4 ILE HD2 59 0.0186 1.008 ; qtot -0.048
60 HC 4 ILE HD3 60 0.0186 1.008 ; qtot -0.0294
61 C 4 ILE C 61 0.5973 12.01 ; qtot 0.5679
62 O 4 ILE O 62 -0.5679 16 ; qtot 0
; residue 5 LEU rtp LEU q 0.0
63 N 5 LEU N 63 -0.4157 14.01 ; qtot -0.4157
64 H 5 LEU H 64 0.2719 1.008 ; qtot -0.1438
65 CT 5 LEU CA 65 -0.0518 12.01 ; qtot -0.1956
66 H1 5 LEU HA 66 0.0922 1.008 ; qtot -0.1034
67 CT 5 LEU CB 67 -0.1102 12.01 ; qtot -0.2136
68 HC 5 LEU HB1 68 0.0457 1.008 ; qtot -0.1679
69 HC 5 LEU HB2 69 0.0457 1.008 ; qtot -0.1222
70 CT 5 LEU CG 70 0.3531 12.01 ; qtot 0.2309
71 HC 5 LEU HG 71 -0.0361 1.008 ; qtot 0.1948
72 CT 5 LEU CD1 72 -0.4121 12.01 ; qtot -0.2173
73 HC 5 LEU HD11 73 0.1 1.008 ; qtot -0.1173
74 HC 5 LEU HD12 74 0.1 1.008 ; qtot -0.0173
75 HC 5 LEU HD13 75 0.1 1.008 ; qtot 0.0827
76 CT 5 LEU CD2 76 -0.4121 12.01 ; qtot -0.3294
77 HC 5 LEU HD21 77 0.1 1.008 ; qtot -0.2294
78 HC 5 LEU HD22 78 0.1 1.008 ; qtot -0.1294
79 HC 5 LEU HD23 79 0.1 1.008 ; qtot -0.0294
80 C 5 LEU C 80 0.5973 12.01 ; qtot 0.5679
81 O 5 LEU O 81 -0.5679 16 ; qtot 0
; residue 6 ASN rtp ASN q 0.0
82 N 6 ASN N 82 -0.4157 14.01 ; qtot -0.4157
83 H 6 ASN H 83 0.2719 1.008 ; qtot -0.1438
84 CT 6 ASN CA 84 0.0143 12.01 ; qtot -0.1295
85 H1 6 ASN HA 85 0.1048 1.008 ; qtot -0.0247
86 CT 6 ASN CB 86 -0.2041 12.01 ; qtot -0.2288
87 HC 6 ASN HB1 87 0.0797 1.008 ; qtot -0.1491
88 HC 6 ASN HB2 88 0.0797 1.008 ; qtot -0.0694
89 C 6 ASN CG 89 0.713 12.01 ; qtot 0.6436
90 O 6 ASN OD1 90 -0.5931 16 ; qtot 0.0505
91 N 6 ASN ND2 91 -0.9191 14.01 ; qtot -0.8686
92 H 6 ASN HD21 92 0.4196 1.008 ; qtot -0.449
93 H 6 ASN HD22 93 0.4196 1.008 ; qtot -0.0294
94 C 6 ASN C 94 0.5973 12.01 ; qtot 0.5679
95 O 6 ASN O 95 -0.5679 16 ; qtot 0
; residue 7 ALA rtp ALA q 0.0
96 N 7 ALA N 96 -0.4157 14.01 ; qtot -0.4157
97 H 7 ALA H 97 0.2719 1.008 ; qtot -0.1438
98 CT 7 ALA CA 98 0.0337 12.01 ; qtot -0.1101
99 H1 7 ALA HA 99 0.0823 1.008 ; qtot -0.0278
100 CT 7 ALA CB 100 -0.1825 12.01 ; qtot -0.2103
101 HC 7 ALA HB1 101 0.0603 1.008 ; qtot -0.15
102 HC 7 ALA HB2 102 0.0603 1.008 ; qtot -0.0897
103 HC 7 ALA HB3 103 0.0603 1.008 ; qtot -0.0294
104 C 7 ALA C 104 0.5973 12.01 ; qtot 0.5679
105 O 7 ALA O 105 -0.5679 16 ; qtot 0
; residue 8 ALA rtp ALA q 0.0
106 N 8 ALA N 106 -0.4157 14.01 ; qtot -0.4157
107 H 8 ALA H 107 0.2719 1.008 ; qtot -0.1438
108 CT 8 ALA CA 108 0.0337 12.01 ; qtot -0.1101
109 H1 8 ALA HA 109 0.0823 1.008 ; qtot -0.0278
110 CT 8 ALA CB 110 -0.1825 12.01 ; qtot -0.2103
111 HC 8 ALA HB1 111 0.0603 1.008 ; qtot -0.15
112 HC 8 ALA HB2 112 0.0603 1.008 ; qtot -0.0897
113 HC 8 ALA HB3 113 0.0603 1.008 ; qtot -0.0294
114 C 8 ALA C 114 0.5973 12.01 ; qtot 0.5679
115 O 8 ALA O 115 -0.5679 16 ; qtot 0
; residue 9 ALA rtp ALA q 0.0
116 N 9 ALA N 116 -0.4157 14.01 ; qtot -0.4157
117 H 9 ALA H 117 0.2719 1.008 ; qtot -0.1438
118 CT 9 ALA CA 118 0.0337 12.01 ; qtot -0.1101
119 H1 9 ALA HA 119 0.0823 1.008 ; qtot -0.0278
120 CT 9 ALA CB 120 -0.1825 12.01 ; qtot -0.2103
121 HC 9 ALA HB1 121 0.0603 1.008 ; qtot -0.15
122 HC 9 ALA HB2 122 0.0603 1.008 ; qtot -0.0897
123 HC 9 ALA HB3 123 0.0603 1.008 ; qtot -0.0294
124 C 9 ALA C 124 0.5973 12.01 ; qtot 0.5679
125 O 9 ALA O 125 -0.5679 16 ; qtot 0
; residue 10 ALA rtp ALA q 0.0
126 N 10 ALA N 126 -0.4157 14.01 ; qtot -0.4157
127 H 10 ALA H 127 0.2719 1.008 ; qtot -0.1438
128 CT 10 ALA CA 128 0.0337 12.01 ; qtot -0.1101
129 H1 10 ALA HA 129 0.0823 1.008 ; qtot -0.0278
130 CT 10 ALA CB 130 -0.1825 12.01 ; qtot -0.2103
131 HC 10 ALA HB1 131 0.0603 1.008 ; qtot -0.15
132 HC 10 ALA HB2 132 0.0603 1.008 ; qtot -0.0897
133 HC 10 ALA HB3 133 0.0603 1.008 ; qtot -0.0294
134 C 10 ALA C 134 0.5973 12.01 ; qtot 0.5679
135 O 10 ALA O 135 -0.5679 16 ; qtot 0
; residue 11 ALA rtp CALA q -1.0
136 N 11 ALA N 136 -0.3821 14.01 ; qtot -0.3821
137 H 11 ALA H 137 0.2681 1.008 ; qtot -0.114
138 CT 11 ALA CA 138 -0.1747 12.01 ; qtot -0.2887
139 H1 11 ALA HA 139 0.1067 1.008 ; qtot -0.182
140 CT 11 ALA CB 140 -0.2093 12.01 ; qtot -0.3913
141 HC 11 ALA HB1 141 0.0764 1.008 ; qtot -0.3149
142 HC 11 ALA HB2 142 0.0764 1.008 ; qtot -0.2385
143 HC 11 ALA HB3 143 0.0764 1.008 ; qtot -0.1621
144 C 11 ALA C 144 0.7731 12.01 ; qtot 0.611
145 O2 11 ALA OC1 145 -0.8055 16 ; qtot -0.1945
146 O2 11 ALA OC2 146 -0.8055 16 ; qtot -1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 11 1
7 8 1
7 9 1
7 10 1
11 12 1
11 13 1
13 14 1
13 15 1
15 16 1
15 17 1
15 30 1
17 18 1
17 19 1
17 23 1
19 20 1
19 21 1
19 22 1
23 24 1
23 25 1
23 26 1
26 27 1
26 28 1
26 29 1
30 31 1
30 32 1
32 33 1
32 34 1
34 35 1
34 36 1
34 42 1
36 37 1
36 38 1
36 39 1
39 40 1
39 41 1
42 43 1
42 44 1
44 45 1
44 46 1
46 47 1
46 48 1
46 61 1
48 49 1
48 50 1
48 54 1
50 51 1
50 52 1
50 53 1
54 55 1
54 56 1
54 57 1
57 58 1
57 59 1
57 60 1
61 62 1
61 63 1
63 64 1
63 65 1
65 66 1
65 67 1
65 80 1
67 68 1
67 69 1
67 70 1
70 71 1
70 72 1
70 76 1
72 73 1
72 74 1
72 75 1
76 77 1
76 78 1
76 79 1
80 81 1
80 82 1
82 83 1
82 84 1
84 85 1
84 86 1
84 94 1
86 87 1
86 88 1
86 89 1
89 90 1
89 91 1
91 92 1
91 93 1
94 95 1
94 96 1
96 97 1
96 98 1
98 99 1
98 100 1
98 104 1
100 101 1
100 102 1
100 103 1
104 105 1
104 106 1
106 107 1
106 108 1
108 109 1
108 110 1
108 114 1
110 111 1
110 112 1
110 113 1
114 115 1
114 116 1
116 117 1
116 118 1
118 119 1
118 120 1
118 124 1
120 121 1
120 122 1
120 123 1
124 125 1
124 126 1
126 127 1
126 128 1
128 129 1
128 130 1
128 134 1
130 131 1
130 132 1
130 133 1
134 135 1
134 136 1
136 137 1
136 138 1
138 139 1
138 140 1
138 144 1
140 141 1
140 142 1
140 143 1
144 145 1
144 146 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
1 10 1
1 12 1
1 13 1
2 6 1
2 7 1
2 11 1
3 6 1
3 7 1
3 11 1
4 6 1
4 7 1
4 11 1
5 14 1
5 15 1
6 8 1
6 9 1
6 10 1
6 12 1
6 13 1
7 12 1
7 13 1
8 11 1
9 11 1
10 11 1
11 16 1
11 17 1
11 30 1
12 14 1
12 15 1
13 18 1
13 19 1
13 23 1
13 31 1
13 32 1
14 16 1
14 17 1
14 30 1
15 20 1
15 21 1
15 22 1
15 24 1
15 25 1
15 26 1
15 33 1
15 34 1
16 18 1
16 19 1
16 23 1
16 31 1
16 32 1
17 27 1
17 28 1
17 29 1
17 31 1
17 32 1
18 20 1
18 21 1
18 22 1
18 24 1
18 25 1
18 26 1
18 30 1
19 24 1
19 25 1
19 26 1
19 30 1
20 23 1
21 23 1
22 23 1
23 30 1
24 27 1
24 28 1
24 29 1
25 27 1
25 28 1
25 29 1
30 35 1
30 36 1
30 42 1
31 33 1
31 34 1
32 37 1
32 38 1
32 39 1
32 43 1
32 44 1
33 35 1
33 36 1
33 42 1
34 40 1
34 41 1
34 45 1
34 46 1
35 37 1
35 38 1
35 39 1
35 43 1
35 44 1
36 43 1
36 44 1
37 40 1
37 41 1
37 42 1
38 40 1
38 41 1
38 42 1
39 42 1
42 47 1
42 48 1
42 61 1
43 45 1
43 46 1
44 49 1
44 50 1
44 54 1
44 62 1
44 63 1
45 47 1
45 48 1
45 61 1
46 51 1
46 52 1
46 53 1
46 55 1
46 56 1
46 57 1
46 64 1
46 65 1
47 49 1
47 50 1
47 54 1
47 62 1
47 63 1
48 58 1
48 59 1
48 60 1
48 62 1
48 63 1
49 51 1
49 52 1
49 53 1
49 55 1
49 56 1
49 57 1
49 61 1
50 55 1
50 56 1
50 57 1
50 61 1
51 54 1
52 54 1
53 54 1
54 61 1
55 58 1
55 59 1
55 60 1
56 58 1
56 59 1
56 60 1
61 66 1
61 67 1
61 80 1
62 64 1
62 65 1
63 68 1
63 69 1
63 70 1
63 81 1
63 82 1
64 66 1
64 67 1
64 80 1
65 71 1
65 72 1
65 76 1
65 83 1
65 84 1
66 68 1
66 69 1
66 70 1
66 81 1
66 82 1
67 73 1
67 74 1
67 75 1
67 77 1
67 78 1
67 79 1
67 81 1
67 82 1
68 71 1
68 72 1
68 76 1
68 80 1
69 71 1
69 72 1
69 76 1
69 80 1
70 80 1
71 73 1
71 74 1
71 75 1
71 77 1
71 78 1
71 79 1
72 77 1
72 78 1
72 79 1
73 76 1
74 76 1
75 76 1
80 85 1
80 86 1
80 94 1
81 83 1
81 84 1
82 87 1
82 88 1
82 89 1
82 95 1
82 96 1
83 85 1
83 86 1
83 94 1
84 90 1
84 91 1
84 97 1
84 98 1
85 87 1
85 88 1
85 89 1
85 95 1
85 96 1
86 92 1
86 93 1
86 95 1
86 96 1
87 90 1
87 91 1
87 94 1
88 90 1
88 91 1
88 94 1
89 94 1
90 92 1
90 93 1
94 99 1
94 100 1
94 104 1
95 97 1
95 98 1
96 101 1
96 102 1
96 103 1
96 105 1
96 106 1
97 99 1
97 100 1
97 104 1
98 107 1
98 108 1
99 101 1
99 102 1
99 103 1
99 105 1
99 106 1
100 105 1
100 106 1
101 104 1
102 104 1
103 104 1
104 109 1
104 110 1
104 114 1
105 107 1
105 108 1
106 111 1
106 112 1
106 113 1
106 115 1
106 116 1
107 109 1
107 110 1
107 114 1
108 117 1
108 118 1
109 111 1
109 112 1
109 113 1
109 115 1
109 116 1
110 115 1
110 116 1
111 114 1
112 114 1
113 114 1
114 119 1
114 120 1
114 124 1
115 117 1
115 118 1
116 121 1
116 122 1
116 123 1
116 125 1
116 126 1
117 119 1
117 120 1
117 124 1
118 127 1
118 128 1
119 121 1
119 122 1
119 123 1
119 125 1
119 126 1
120 125 1
120 126 1
121 124 1
122 124 1
123 124 1
124 129 1
124 130 1
124 134 1
125 127 1
125 128 1
126 131 1
126 132 1
126 133 1
126 135 1
126 136 1
127 129 1
127 130 1
127 134 1
128 137 1
128 138 1
129 131 1
129 132 1
129 133 1
129 135 1
129 136 1
130 135 1
130 136 1
131 134 1
132 134 1
133 134 1
134 139 1
134 140 1
134 144 1
135 137 1
135 138 1
136 141 1
136 142 1
136 143 1
136 145 1
136 146 1
137 139 1
137 140 1
137 144 1
139 141 1
139 142 1
139 143 1
139 145 1
139 146 1
140 145 1
140 146 1
141 144 1
142 144 1
143 144 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 11 1
6 5 7 1
6 5 11 1
7 5 11 1
5 7 8 1
5 7 9 1
5 7 10 1
8 7 9 1
8 7 10 1
9 7 10 1
5 11 12 1
5 11 13 1
12 11 13 1
11 13 14 1
11 13 15 1
14 13 15 1
13 15 16 1
13 15 17 1
13 15 30 1
16 15 17 1
16 15 30 1
17 15 30 1
15 17 18 1
15 17 19 1
15 17 23 1
18 17 19 1
18 17 23 1
19 17 23 1
17 19 20 1
17 19 21 1
17 19 22 1
20 19 21 1
20 19 22 1
21 19 22 1
17 23 24 1
17 23 25 1
17 23 26 1
24 23 25 1
24 23 26 1
25 23 26 1
23 26 27 1
23 26 28 1
23 26 29 1
27 26 28 1
27 26 29 1
28 26 29 1
15 30 31 1
15 30 32 1
31 30 32 1
30 32 33 1
30 32 34 1
33 32 34 1
32 34 35 1
32 34 36 1
32 34 42 1
35 34 36 1
35 34 42 1
36 34 42 1
34 36 37 1
34 36 38 1
34 36 39 1
37 36 38 1
37 36 39 1
38 36 39 1
36 39 40 1
36 39 41 1
40 39 41 1
34 42 43 1
34 42 44 1
43 42 44 1
42 44 45 1
42 44 46 1
45 44 46 1
44 46 47 1
44 46 48 1
44 46 61 1
47 46 48 1
47 46 61 1
48 46 61 1
46 48 49 1
46 48 50 1
46 48 54 1
49 48 50 1
49 48 54 1
50 48 54 1
48 50 51 1
48 50 52 1
48 50 53 1
51 50 52 1
51 50 53 1
52 50 53 1
48 54 55 1
48 54 56 1
48 54 57 1
55 54 56 1
55 54 57 1
56 54 57 1
54 57 58 1
54 57 59 1
54 57 60 1
58 57 59 1
58 57 60 1
59 57 60 1
46 61 62 1
46 61 63 1
62 61 63 1
61 63 64 1
61 63 65 1
64 63 65 1
63 65 66 1
63 65 67 1
63 65 80 1
66 65 67 1
66 65 80 1
67 65 80 1
65 67 68 1
65 67 69 1
65 67 70 1
68 67 69 1
68 67 70 1
69 67 70 1
67 70 71 1
67 70 72 1
67 70 76 1
71 70 72 1
71 70 76 1
72 70 76 1
70 72 73 1
70 72 74 1
70 72 75 1
73 72 74 1
73 72 75 1
74 72 75 1
70 76 77 1
70 76 78 1
70 76 79 1
77 76 78 1
77 76 79 1
78 76 79 1
65 80 81 1
65 80 82 1
81 80 82 1
80 82 83 1
80 82 84 1
83 82 84 1
82 84 85 1
82 84 86 1
82 84 94 1
85 84 86 1
85 84 94 1
86 84 94 1
84 86 87 1
84 86 88 1
84 86 89 1
87 86 88 1
87 86 89 1
88 86 89 1
86 89 90 1
86 89 91 1
90 89 91 1
89 91 92 1
89 91 93 1
92 91 93 1
84 94 95 1
84 94 96 1
95 94 96 1
94 96 97 1
94 96 98 1
97 96 98 1
96 98 99 1
96 98 100 1
96 98 104 1
99 98 100 1
99 98 104 1
100 98 104 1
98 100 101 1
98 100 102 1
98 100 103 1
101 100 102 1
101 100 103 1
102 100 103 1
98 104 105 1
98 104 106 1
105 104 106 1
104 106 107 1
104 106 108 1
107 106 108 1
106 108 109 1
106 108 110 1
106 108 114 1
109 108 110 1
109 108 114 1
110 108 114 1
108 110 111 1
108 110 112 1
108 110 113 1
111 110 112 1
111 110 113 1
112 110 113 1
108 114 115 1
108 114 116 1
115 114 116 1
114 116 117 1
114 116 118 1
117 116 118 1
116 118 119 1
116 118 120 1
116 118 124 1
119 118 120 1
119 118 124 1
120 118 124 1
118 120 121 1
118 120 122 1
118 120 123 1
121 120 122 1
121 120 123 1
122 120 123 1
118 124 125 1
118 124 126 1
125 124 126 1
124 126 127 1
124 126 128 1
127 126 128 1
126 128 129 1
126 128 130 1
126 128 134 1
129 128 130 1
129 128 134 1
130 128 134 1
128 130 131 1
128 130 132 1
128 130 133 1
131 130 132 1
131 130 133 1
132 130 133 1
128 134 135 1
128 134 136 1
135 134 136 1
134 136 137 1
134 136 138 1
137 136 138 1
136 138 139 1
136 138 140 1
136 138 144 1
139 138 140 1
139 138 144 1
140 138 144 1
138 140 141 1
138 140 142 1
138 140 143 1
141 140 142 1
141 140 143 1
142 140 143 1
138 144 145 1
138 144 146 1
145 144 146 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 9
2 1 5 7 9
2 1 5 11 9
3 1 5 6 9
3 1 5 7 9
3 1 5 11 9
4 1 5 6 9
4 1 5 7 9
4 1 5 11 9
1 5 7 8 9
1 5 7 9 9
1 5 7 10 9
6 5 7 8 9
6 5 7 9 9
6 5 7 10 9
11 5 7 8 9
11 5 7 9 9
11 5 7 10 9
1 5 11 12 9
1 5 11 13 9
6 5 11 12 9
6 5 11 13 9
7 5 11 12 9
7 5 11 13 9
5 11 13 14 9
5 11 13 15 9
12 11 13 14 9
12 11 13 15 9
11 13 15 16 9
11 13 15 17 9
11 13 15 30 9
14 13 15 16 9
14 13 15 17 9
14 13 15 30 9
13 15 17 19 9 torsion_ILE_N_CA_CB_CG2_mult1
13 15 17 18 9
13 15 17 23 9
16 15 17 18 9
16 15 17 19 9
16 15 17 23 9
30 15 17 18 9
30 15 17 19 9
30 15 17 23 9
13 15 30 31 9
13 15 30 32 9
16 15 30 31 9
16 15 30 32 9
17 15 30 31 9
17 15 30 32 9
15 17 19 20 9
15 17 19 21 9
15 17 19 22 9
18 17 19 20 9
18 17 19 21 9
18 17 19 22 9
23 17 19 20 9
23 17 19 21 9
23 17 19 22 9
15 17 23 24 9
15 17 23 25 9
15 17 23 26 9
18 17 23 24 9
18 17 23 25 9
18 17 23 26 9
19 17 23 24 9
19 17 23 25 9
19 17 23 26 9
17 23 26 27 9
17 23 26 28 9
17 23 26 29 9
24 23 26 27 9
24 23 26 28 9
24 23 26 29 9
25 23 26 27 9
25 23 26 28 9
25 23 26 29 9
15 30 32 33 9
15 30 32 34 9
31 30 32 33 9
31 30 32 34 9
30 32 34 35 9
30 32 34 36 9
30 32 34 42 9
33 32 34 35 9
33 32 34 36 9
33 32 34 42 9
32 34 36 39 9 torsion_ASP_N_CA_CB_CG_mult1
32 34 36 37 9
32 34 36 38 9
35 34 36 37 9
35 34 36 38 9
35 34 36 39 9
42 34 36 37 9
42 34 36 38 9
42 34 36 39 9
32 34 42 43 9
32 34 42 44 9
35 34 42 43 9
35 34 42 44 9
36 34 42 43 9
36 34 42 44 9
34 36 39 40 9 torsion_ASP_CA_CB_CG_OD_mult1
34 36 39 41 9 torsion_ASP_CA_CB_CG_OD_mult1
37 36 39 40 9
37 36 39 41 9
38 36 39 40 9
38 36 39 41 9
34 42 44 45 9
34 42 44 46 9
43 42 44 45 9
43 42 44 46 9
42 44 46 47 9
42 44 46 48 9
42 44 46 61 9
45 44 46 47 9
45 44 46 48 9
45 44 46 61 9
44 46 48 50 9 torsion_ILE_N_CA_CB_CG2_mult1
44 46 48 49 9
44 46 48 54 9
47 46 48 49 9
47 46 48 50 9
47 46 48 54 9
61 46 48 49 9
61 46 48 50 9
61 46 48 54 9
44 46 61 62 9
44 46 61 63 9
47 46 61 62 9
47 46 61 63 9
48 46 61 62 9
48 46 61 63 9
46 48 50 51 9
46 48 50 52 9
46 48 50 53 9
49 48 50 51 9
49 48 50 52 9
49 48 50 53 9
54 48 50 51 9
54 48 50 52 9
54 48 50 53 9
46 48 54 55 9
46 48 54 56 9
46 48 54 57 9
49 48 54 55 9
49 48 54 56 9
49 48 54 57 9
50 48 54 55 9
50 48 54 56 9
50 48 54 57 9
48 54 57 58 9
48 54 57 59 9
48 54 57 60 9
55 54 57 58 9
55 54 57 59 9
55 54 57 60 9
56 54 57 58 9
56 54 57 59 9
56 54 57 60 9
46 61 63 64 9
46 61 63 65 9
62 61 63 64 9
62 61 63 65 9
61 63 65 66 9
61 63 65 67 9
61 63 65 80 9
64 63 65 66 9
64 63 65 67 9
64 63 65 80 9
80 65 67 70 9 torsion_LEU_C_CA_CB_CG_mult1
63 65 67 68 9
63 65 67 69 9
63 65 67 70 9
66 65 67 68 9
66 65 67 69 9
66 65 67 70 9
80 65 67 68 9
80 65 67 69 9
63 65 80 81 9
63 65 80 82 9
66 65 80 81 9
66 65 80 82 9
67 65 80 81 9
67 65 80 82 9
65 67 70 71 9
65 67 70 72 9
65 67 70 76 9
68 67 70 71 9
68 67 70 72 9
68 67 70 76 9
69 67 70 71 9
69 67 70 72 9
69 67 70 76 9
67 70 72 73 9
67 70 72 74 9
67 70 72 75 9
71 70 72 73 9
71 70 72 74 9
71 70 72 75 9
76 70 72 73 9
76 70 72 74 9
76 70 72 75 9
67 70 76 77 9
67 70 76 78 9
67 70 76 79 9
71 70 76 77 9
71 70 76 78 9
71 70 76 79 9
72 70 76 77 9
72 70 76 78 9
72 70 76 79 9
65 80 82 83 9
65 80 82 84 9
81 80 82 83 9
81 80 82 84 9
80 82 84 85 9
80 82 84 86 9
80 82 84 94 9
83 82 84 85 9
83 82 84 86 9
83 82 84 94 9
94 84 86 89 9 torsion_ASN_C_CA_CB_CG_mult1
82 84 86 87 9
82 84 86 88 9
82 84 86 89 9
85 84 86 87 9
85 84 86 88 9
85 84 86 89 9
94 84 86 87 9
94 84 86 88 9
82 84 94 95 9
82 84 94 96 9
85 84 94 95 9
85 84 94 96 9
86 84 94 95 9
86 84 94 96 9
84 86 89 91 9 torsion_ASN_CA_CB_CG_ND2_mult1
84 86 89 90 9
87 86 89 90 9
87 86 89 91 9
88 86 89 90 9
88 86 89 91 9
86 89 91 92 9
86 89 91 93 9
90 89 91 92 9
90 89 91 93 9
84 94 96 97 9
84 94 96 98 9
95 94 96 97 9
95 94 96 98 9
94 96 98 99 9
94 96 98 100 9
94 96 98 104 9
97 96 98 99 9
97 96 98 100 9
97 96 98 104 9
96 98 100 101 9
96 98 100 102 9
96 98 100 103 9
99 98 100 101 9
99 98 100 102 9
99 98 100 103 9
104 98 100 101 9
104 98 100 102 9
104 98 100 103 9
96 98 104 105 9
96 98 104 106 9
99 98 104 105 9
99 98 104 106 9
100 98 104 105 9
100 98 104 106 9
98 104 106 107 9
98 104 106 108 9
105 104 106 107 9
105 104 106 108 9
104 106 108 109 9
104 106 108 110 9
104 106 108 114 9
107 106 108 109 9
107 106 108 110 9
107 106 108 114 9
106 108 110 111 9
106 108 110 112 9
106 108 110 113 9
109 108 110 111 9
109 108 110 112 9
109 108 110 113 9
114 108 110 111 9
114 108 110 112 9
114 108 110 113 9
106 108 114 115 9
106 108 114 116 9
109 108 114 115 9
109 108 114 116 9
110 108 114 115 9
110 108 114 116 9
108 114 116 117 9
108 114 116 118 9
115 114 116 117 9
115 114 116 118 9
114 116 118 119 9
114 116 118 120 9
114 116 118 124 9
117 116 118 119 9
117 116 118 120 9
117 116 118 124 9
116 118 120 121 9
116 118 120 122 9
116 118 120 123 9
119 118 120 121 9
119 118 120 122 9
119 118 120 123 9
124 118 120 121 9
124 118 120 122 9
124 118 120 123 9
116 118 124 125 9
116 118 124 126 9
119 118 124 125 9
119 118 124 126 9
120 118 124 125 9
120 118 124 126 9
118 124 126 127 9
118 124 126 128 9
125 124 126 127 9
125 124 126 128 9
124 126 128 129 9
124 126 128 130 9
124 126 128 134 9
127 126 128 129 9
127 126 128 130 9
127 126 128 134 9
126 128 130 131 9
126 128 130 132 9
126 128 130 133 9
129 128 130 131 9
129 128 130 132 9
129 128 130 133 9
134 128 130 131 9
134 128 130 132 9
134 128 130 133 9
126 128 134 135 9
126 128 134 136 9
129 128 134 135 9
129 128 134 136 9
130 128 134 135 9
130 128 134 136 9
128 134 136 137 9
128 134 136 138 9
135 134 136 137 9
135 134 136 138 9
134 136 138 139 9
134 136 138 140 9
134 136 138 144 9
137 136 138 139 9
137 136 138 140 9
137 136 138 144 9
136 138 140 141 9
136 138 140 142 9
136 138 140 143 9
139 138 140 141 9
139 138 140 142 9
139 138 140 143 9
144 138 140 141 9
144 138 140 142 9
144 138 140 143 9
136 138 144 145 9
136 138 144 146 9
139 138 144 145 9
139 138 144 146 9
140 138 144 145 9
140 138 144 146 9
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 13 11 12 4
11 15 13 14 4
15 32 30 31 4
30 34 32 33 4
34 44 42 43 4
36 40 39 41 4
42 46 44 45 4
46 63 61 62 4
61 65 63 64 4
65 82 80 81 4
80 84 82 83 4
84 96 94 95 4
86 91 89 90 4
89 92 91 93 4
94 98 96 97 4
98 106 104 105 4
104 108 106 107 4
108 116 114 115 4
114 118 116 117 4
118 126 124 125 4
124 128 126 127 4
128 136 134 135 4
134 138 136 137 4
138 145 144 146 4
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber99sb-ildn.ff/tip4pew.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein 1
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