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Unverified Commit 25f4e982 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Support GROMACS files that use GROMOS force fields (#4028) 



* Support GROMOS bond and angle types

* Support NBFIX with geometric combining rule

* Continuing GROMOS support

* Bug fixes

* Fixes to test case

* Update wrappers/python/openmm/app/gromacstopfile.py
Co-authored-by: default avatarJason Swails <jason@entos.ai>

* Improve logic for handling dihedraltypes

---------
Co-authored-by: default avatarJason Swails <jason@entos.ai>
parent 0c7f2501
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wrappers/python/openmm/app/gromacstopfile.py
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...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2022 Stanford University and the Authors. Portions copyright (c) 2012-2023 Stanford University and the Authors.
Authors: Peter Eastman Authors: Peter Eastman
Contributors: Jason Swails Contributors: Jason Swails
...@@ -45,6 +45,7 @@ import re ...@@ -45,6 +45,7 @@ import re
import distutils.spawn import distutils.spawn
from collections import OrderedDict, defaultdict from collections import OrderedDict, defaultdict
from itertools import combinations, combinations_with_replacement from itertools import combinations, combinations_with_replacement
from copy import deepcopy
HBonds = ff.HBonds HBonds = ff.HBonds
AllBonds = ff.AllBonds AllBonds = ff.AllBonds
...@@ -108,7 +109,9 @@ class GromacsTopFile(object): ...@@ -108,7 +109,9 @@ class GromacsTopFile(object):
class _MoleculeType(object): class _MoleculeType(object):
"""Inner class to store information about a molecule type.""" """Inner class to store information about a molecule type."""
def __init__(self): def __init__(self, name, nrexcl):
self.name = name
self.nrexcl = nrexcl
self.atoms = [] self.atoms = []
self.bonds = [] self.bonds = []
self.angles = [] self.angles = []
...@@ -122,6 +125,41 @@ class GromacsTopFile(object): ...@@ -122,6 +125,41 @@ class GromacsTopFile(object):
self.has_virtual_sites = False self.has_virtual_sites = False
self.has_nbfix_terms = False self.has_nbfix_terms = False
def findExclusionsFromBonds(self, genpairs):
"""Find exclusions between atoms separated by up to nrexcl bonds if genpairs is false,
or up to 2 bonds if genpairs is true.
"""
bondedTo = [set() for i in range(len(self.atoms))]
for fields in self.bonds:
i = int(fields[0])-1
j = int(fields[1])-1
bondedTo[i].add(j)
bondedTo[j].add(i)
# Identify all neighbors of each atom with each separation.
bondedWithSeparation = [bondedTo]
maxBonds = self.nrexcl
if genpairs:
maxBonds = min(maxBonds, 2)
for i in range(maxBonds-1):
lastBonds = bondedWithSeparation[-1]
newBonds = deepcopy(lastBonds)
for atom in range(len(self.atoms)):
for a1 in lastBonds[atom]:
for a2 in bondedTo[a1]:
newBonds[atom].add(a2)
bondedWithSeparation.append(newBonds)
# Build the list of pairs.
pairs = []
for atom in range(len(self.atoms)):
for otherAtom in bondedWithSeparation[-1][atom]:
if otherAtom > atom:
pairs.append((atom, otherAtom))
return pairs
def _processFile(self, file): def _processFile(self, file):
append = '' append = ''
for line in open(file): for line in open(file):
...@@ -291,7 +329,7 @@ class GromacsTopFile(object): ...@@ -291,7 +329,7 @@ class GromacsTopFile(object):
fields = line.split() fields = line.split()
if len(fields) < 1: if len(fields) < 1:
raise ValueError('Too few fields in [ moleculetypes ] line: '+line) raise ValueError('Too few fields in [ moleculetypes ] line: '+line)
type = GromacsTopFile._MoleculeType() type = GromacsTopFile._MoleculeType(fields[0], int(fields[1]))
self._moleculeTypes[fields[0]] = type self._moleculeTypes[fields[0]] = type
self._currentMoleculeType = type self._currentMoleculeType = type
...@@ -318,8 +356,8 @@ class GromacsTopFile(object): ...@@ -318,8 +356,8 @@ class GromacsTopFile(object):
fields = line.split() fields = line.split()
if len(fields) < 3: if len(fields) < 3:
raise ValueError('Too few fields in [ bonds ] line: '+line) raise ValueError('Too few fields in [ bonds ] line: '+line)
if fields[2] != '1': if fields[2] not in ('1', '2'):
raise ValueError('Unsupported function type in [ bonds ] line: '+line) raise ValueError('Unsupported function type in [ bonds ] line: '+line)
self._currentMoleculeType.bonds.append(fields) self._currentMoleculeType.bonds.append(fields)
def _processAngle(self, line): def _processAngle(self, line):
...@@ -329,7 +367,7 @@ class GromacsTopFile(object): ...@@ -329,7 +367,7 @@ class GromacsTopFile(object):
fields = line.split() fields = line.split()
if len(fields) < 4: if len(fields) < 4:
raise ValueError('Too few fields in [ angles ] line: '+line) raise ValueError('Too few fields in [ angles ] line: '+line)
if fields[3] not in ('1', '5'): if fields[3] not in ('1', '2', '5'):
raise ValueError('Unsupported function type in [ angles ] line: '+line) raise ValueError('Unsupported function type in [ angles ] line: '+line)
self._currentMoleculeType.angles.append(fields) self._currentMoleculeType.angles.append(fields)
...@@ -405,22 +443,26 @@ class GromacsTopFile(object): ...@@ -405,22 +443,26 @@ class GromacsTopFile(object):
fields = line.split() fields = line.split()
if len(fields) < 5: if len(fields) < 5:
raise ValueError('Too few fields in [ bondtypes ] line: '+line) raise ValueError('Too few fields in [ bondtypes ] line: '+line)
if fields[2] != '1': if fields[2] not in ('1', '2'):
raise ValueError('Unsupported function type in [ bondtypes ] line: '+line) raise ValueError('Unsupported function type in [ bondtypes ] line: '+line)
self._bondTypes[tuple(fields[:2])] = fields self._bondTypes[tuple(fields[:3])] = fields
def _processAngleType(self, line): def _processAngleType(self, line):
"""Process a line in the [ angletypes ] category.""" """Process a line in the [ angletypes ] category."""
fields = line.split() fields = line.split()
if len(fields) < 6: if len(fields) < 6:
raise ValueError('Too few fields in [ angletypes ] line: '+line) raise ValueError('Too few fields in [ angletypes ] line: '+line)
if fields[3] not in ('1', '5'): if fields[3] not in ('1', '2', '5'):
raise ValueError('Unsupported function type in [ angletypes ] line: '+line) raise ValueError('Unsupported function type in [ angletypes ] line: '+line)
self._angleTypes[tuple(fields[:3])] = fields self._angleTypes[tuple(fields[:3])] = fields
def _processDihedralType(self, line): def _processDihedralType(self, line):
"""Process a line in the [ dihedraltypes ] category.""" """Process a line in the [ dihedraltypes ] category."""
fields = line.split() fields = line.split()
if len(fields[2]) == 1 and fields[2].isdigit():
# The third field contains the function type, meaning only two atom types are specified.
# Interpret them as the two inner ones.
fields = ['X', fields[0], fields[1], 'X']+fields[2:]
if len(fields) < 7: if len(fields) < 7:
raise ValueError('Too few fields in [ dihedraltypes ] line: '+line) raise ValueError('Too few fields in [ dihedraltypes ] line: '+line)
if fields[4] not in ('1', '2', '3', '4', '5', '9'): if fields[4] not in ('1', '2', '3', '4', '5', '9'):
...@@ -654,6 +696,17 @@ class GromacsTopFile(object): ...@@ -654,6 +696,17 @@ class GromacsTopFile(object):
System System
the newly created System the newly created System
""" """
# Build a list of atom types for NBFIX
atom_types = []
for moleculeName, moleculeCount in self._molecules:
moleculeType = self._moleculeTypes[moleculeName]
for _ in range(moleculeCount):
for atom in moleculeType.atoms:
atom_types.append(atom[1])
has_nbfix_terms = any([pair in self._nonbondTypes for pair in combinations_with_replacement(sorted(set(atom_types)), 2)])
# Create the System. # Create the System.
sys = mm.System() sys = mm.System()
...@@ -664,7 +717,12 @@ class GromacsTopFile(object): ...@@ -664,7 +717,12 @@ class GromacsTopFile(object):
raise ValueError('Illegal nonbonded method for a non-periodic system') raise ValueError('Illegal nonbonded method for a non-periodic system')
nb = mm.NonbondedForce() nb = mm.NonbondedForce()
sys.addForce(nb) sys.addForce(nb)
if self._defaults[1] in ('1', '3'): lj = None
if has_nbfix_terms:
lj = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6; a=acoef(type1, type2); b=bcoef(type1, type2)')
lj.addPerParticleParameter('type')
sys.addForce(lj)
elif self._defaults[1] in ('1', '3'):
lj = mm.CustomNonbondedForce('A1*A2/r^12-C1*C2/r^6') lj = mm.CustomNonbondedForce('A1*A2/r^12-C1*C2/r^6')
lj.addPerParticleParameter('C') lj.addPerParticleParameter('C')
lj.addPerParticleParameter('A') lj.addPerParticleParameter('A')
...@@ -677,8 +735,8 @@ class GromacsTopFile(object): ...@@ -677,8 +735,8 @@ class GromacsTopFile(object):
nb.setReactionFieldDielectric(1.0) nb.setReactionFieldDielectric(1.0)
elif implicitSolvent is not None: elif implicitSolvent is not None:
raise ValueError('Illegal value for implicitSolvent') raise ValueError('Illegal value for implicitSolvent')
bonds = None bonds = {}
angles = None angles = {}
periodic = None periodic = None
rb = None rb = None
harmonicTorsion = None harmonicTorsion = None
...@@ -709,16 +767,6 @@ class GromacsTopFile(object): ...@@ -709,16 +767,6 @@ class GromacsTopFile(object):
for types in dihedralTypeTable.values(): for types in dihedralTypeTable.values():
types.append(key) types.append(key)
# NBFIX
atom_types = []
for moleculeName, moleculeCount in self._molecules:
moleculeType = self._moleculeTypes[moleculeName]
for _ in range(moleculeCount):
for atom in moleculeType.atoms:
atom_types.append(atom[1])
has_nbfix_terms = any([pair in self._nonbondTypes for pair in combinations_with_replacement(sorted(set(atom_types)), 2)])
if has_nbfix_terms: if has_nbfix_terms:
# Build a lookup table and angle/dihedral indices list to # Build a lookup table and angle/dihedral indices list to
# let us handle exclusion manually. # let us handle exclusion manually.
...@@ -731,6 +779,7 @@ class GromacsTopFile(object): ...@@ -731,6 +779,7 @@ class GromacsTopFile(object):
for moleculeName, moleculeCount in self._molecules: for moleculeName, moleculeCount in self._molecules:
moleculeType = self._moleculeTypes[moleculeName] moleculeType = self._moleculeTypes[moleculeName]
exclusionsFromBonds = moleculeType.findExclusionsFromBonds(self._genpairs)
for i in range(moleculeCount): for i in range(moleculeCount):
# Record the types of all atoms. # Record the types of all atoms.
...@@ -758,12 +807,15 @@ class GromacsTopFile(object): ...@@ -758,12 +807,15 @@ class GromacsTopFile(object):
for fields in moleculeType.bonds: for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]] atoms = [int(x)-1 for x in fields[:2]]
types = tuple(bondedTypes[i] for i in atoms) types = tuple(bondedTypes[i] for i in atoms)
bondType = fields[2]
reversedTypes = types[::-1]+(bondType,)
types = types+(bondType,)
if len(fields) >= 5: if len(fields) >= 5:
params = fields[3:5] params = fields[3:5]
elif types in self._bondTypes: elif types in self._bondTypes:
params = self._bondTypes[types][3:5] params = self._bondTypes[types][3:5]
elif types[::-1] in self._bondTypes: elif reversedTypes in self._bondTypes:
params = self._bondTypes[types[::-1]][3:5] params = self._bondTypes[reversedTypes][3:5]
else: else:
raise ValueError('No parameters specified for bond: '+fields[0]+', '+fields[1]) raise ValueError('No parameters specified for bond: '+fields[0]+', '+fields[1])
# Decide whether to use a constraint or a bond. # Decide whether to use a constraint or a bond.
...@@ -780,11 +832,21 @@ class GromacsTopFile(object): ...@@ -780,11 +832,21 @@ class GromacsTopFile(object):
length = float(params[0]) length = float(params[0])
if useConstraint: if useConstraint:
sys.addConstraint(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], length) sys.addConstraint(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], length)
elif bondType == '1':
if bondType not in bonds:
bonds[bondType] = mm.HarmonicBondForce()
sys.addForce(bonds[bondType])
bonds[bondType].addBond(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], length, float(params[1]))
elif bondType == '2':
if bondType not in bonds:
bonds[bondType] = mm.CustomBondForce('0.25*k*(r^2-r0^2)^2')
bonds[bondType].addPerBondParameter('r0')
bonds[bondType].addPerBondParameter('k')
bonds[bondType].setName('GROMOSBondForce')
sys.addForce(bonds[bondType])
bonds[bondType].addBond(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], (length, float(params[1])))
else: else:
if bonds is None: raise ValueError('Internal error: bondType has unexpected value: '+bondType)
bonds = mm.HarmonicBondForce()
sys.addForce(bonds)
bonds.addBond(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], length, float(params[1]))
# Record information that will be needed for constraining angles. # Record information that will be needed for constraining angles.
atomBonds[atoms[0]][atoms[1]] = length atomBonds[atoms[0]][atoms[1]] = length
atomBonds[atoms[1]][atoms[0]] = length atomBonds[atoms[1]][atoms[0]] = length
...@@ -795,6 +857,7 @@ class GromacsTopFile(object): ...@@ -795,6 +857,7 @@ class GromacsTopFile(object):
for fields in moleculeType.angles: for fields in moleculeType.angles:
atoms = [int(x)-1 for x in fields[:3]] atoms = [int(x)-1 for x in fields[:3]]
types = tuple(bondedTypes[i] for i in atoms) types = tuple(bondedTypes[i] for i in atoms)
angleType = fields[3]
if len(fields) >= 6: if len(fields) >= 6:
params = fields[4:] params = fields[4:]
elif types in self._angleTypes: elif types in self._angleTypes:
...@@ -823,18 +886,29 @@ class GromacsTopFile(object): ...@@ -823,18 +886,29 @@ class GromacsTopFile(object):
length = math.sqrt(l1*l1 + l2*l2 - 2*l1*l2*math.cos(theta)) length = math.sqrt(l1*l1 + l2*l2 - 2*l1*l2*math.cos(theta))
sys.addConstraint(baseAtomIndex+atoms[0], baseAtomIndex+atoms[2], length) sys.addConstraint(baseAtomIndex+atoms[0], baseAtomIndex+atoms[2], length)
else: else:
if angles is None: if angleType in ('1', '5'):
angles = mm.HarmonicAngleForce() if angleType not in angles:
sys.addForce(angles) angles[angleType] = mm.HarmonicAngleForce()
angles.addAngle(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], theta, float(params[1])) sys.addForce(angles[angleType])
if fields[3] == '5': angles[angleType].addAngle(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], theta, float(params[1]))
# This is a Urey-Bradley term, so add the bond. if angleType == '5':
if bonds is None: # This is a Urey-Bradley term, so also add the bond.
bonds = mm.HarmonicBondForce() if '1' not in bonds:
sys.addForce(bonds) bonds['1'] = mm.HarmonicBondForce()
k = float(params[3]) sys.addForce(bonds['1'])
if k != 0: k = float(params[3])
bonds.addBond(baseAtomIndex+atoms[0], baseAtomIndex+atoms[2], float(params[2]), k) if k != 0:
bonds['1'].addBond(baseAtomIndex + atoms[0], baseAtomIndex + atoms[2], float(params[2]), k)
elif angleType == '2':
if angleType not in angles:
angles[angleType] = mm.CustomAngleForce('0.5*k*(cos(theta)-cos(theta0))^2')
angles[angleType].addPerAngleParameter('theta0')
angles[angleType].addPerAngleParameter('k')
angles[angleType].setName('GROMOSAngleForce')
sys.addForce(angles[angleType])
angles[angleType].addAngle(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], (theta, float(params[1])))
else:
raise ValueError('Internal error: angleType has unexpected value: '+angleType)
# Add torsions. # Add torsions.
...@@ -878,6 +952,7 @@ class GromacsTopFile(object): ...@@ -878,6 +952,7 @@ class GromacsTopFile(object):
harmonicTorsion = mm.CustomTorsionForce('0.5*k*(thetap-theta0)^2; thetap = step(-(theta-theta0+pi))*2*pi+theta+step(theta-theta0-pi)*(-2*pi); pi = %.15g' % math.pi) harmonicTorsion = mm.CustomTorsionForce('0.5*k*(thetap-theta0)^2; thetap = step(-(theta-theta0+pi))*2*pi+theta+step(theta-theta0-pi)*(-2*pi); pi = %.15g' % math.pi)
harmonicTorsion.addPerTorsionParameter('theta0') harmonicTorsion.addPerTorsionParameter('theta0')
harmonicTorsion.addPerTorsionParameter('k') harmonicTorsion.addPerTorsionParameter('k')
harmonicTorsion.setName('HarmonicTorsionForce')
sys.addForce(harmonicTorsion) sys.addForce(harmonicTorsion)
# map phi0 into correct space # map phi0 into correct space
phi0 = phi0 - 360 if phi0 > 180 else phi0 phi0 = phi0 - 360 if phi0 > 180 else phi0
...@@ -934,10 +1009,9 @@ class GromacsTopFile(object): ...@@ -934,10 +1009,9 @@ class GromacsTopFile(object):
q = float(params[4]) q = float(params[4])
if has_nbfix_terms: if has_nbfix_terms:
if self._defaults[1] != '2':
raise NotImplementedError('NBFIX terms with LB combination rule is not yet supported')
nb.addParticle(q, 1.0, 0.0) nb.addParticle(q, 1.0, 0.0)
atom_charges.append(q) atom_charges.append(q)
lj.addParticle([0])
else: else:
if self._defaults[1] == '1': if self._defaults[1] == '1':
nb.addParticle(q, 1.0, 0.0) nb.addParticle(q, 1.0, 0.0)
...@@ -1013,6 +1087,8 @@ class GromacsTopFile(object): ...@@ -1013,6 +1087,8 @@ class GromacsTopFile(object):
atoms = [int(x)-1 for x in fields] atoms = [int(x)-1 for x in fields]
for atom in atoms[1:]: for atom in atoms[1:]:
exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom)) exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom))
for atoms in exclusionsFromBonds:
exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1]))
# Record virtual sites # Record virtual sites
...@@ -1059,9 +1135,12 @@ class GromacsTopFile(object): ...@@ -1059,9 +1135,12 @@ class GromacsTopFile(object):
rmin4 = float(params4[6]) rmin4 = float(params4[6])
eps4 = float(params4[7]) eps4 = float(params4[7])
charge_prod = (q1*q4) charge_prod = fudgeQQ*q1*q4
epsilon = (math.sqrt(abs(eps1 * eps4))) epsilon = math.sqrt(abs(eps1 * eps4))
rmin14 = (rmin1 + rmin4) / 2 if self._defaults[1] == '2':
rmin14 = (rmin1 + rmin4) / 2
else:
rmin14 = math.sqrt(rmin1 * rmin4)
nb.addException(tor[0], tor[3], charge_prod, rmin14, epsilon) nb.addException(tor[0], tor[3], charge_prod, rmin14, epsilon)
excluded_atom_pairs.add(key) excluded_atom_pairs.add(key)
...@@ -1087,23 +1166,21 @@ class GromacsTopFile(object): ...@@ -1087,23 +1166,21 @@ class GromacsTopFile(object):
for exclusion in exclusions: for exclusion in exclusions:
nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True) nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True)
if self._defaults[1] in ('1', '3'): if lj is not None:
# We're using a CustomNonbondedForce for LJ interactions, so also create a CustomBondForce # We're using a CustomNonbondedForce for LJ interactions, so also create a CustomBondForce
# to handle the exceptions. # to handle the exceptions.
pair_bond = mm.CustomBondForce('-C/r^6+A/r^12') pair_bond = mm.CustomBondForce('-C/r^6+A/r^12')
pair_bond.addPerBondParameter('C') pair_bond.addPerBondParameter('C')
pair_bond.addPerBondParameter('A') pair_bond.addPerBondParameter('A')
pair_bond.setName('LennardJonesExceptions')
sys.addForce(pair_bond) sys.addForce(pair_bond)
lj.createExclusionsFromBonds(bondIndices, 3)
for pair in pairs: for pair in pairs:
nb.addException(pair[0], pair[1], pair[2], 1.0, 0.0, True) nb.addException(pair[0], pair[1], pair[2], 1.0, 0.0, True)
pair_bond.addBond(pair[0], pair[1], [pair[3], pair[4]]) pair_bond.addBond(pair[0], pair[1], [pair[3], pair[4]])
existing = set(tuple(lj.getExclusionParticles(i)) for i in range(lj.getNumExclusions())) for i in range(nb.getNumExceptions()):
for exclusion in exclusions: ii, jj, q, eps, sig = nb.getExceptionParameters(i)
if exclusion not in existing and tuple(reversed(exclusion)) not in existing: lj.addExclusion(ii, jj)
lj.addExclusion(exclusion[0], exclusion[1])
existing.add(exclusion)
elif self._defaults[1] == '2': elif self._defaults[1] == '2':
for pair in pairs: for pair in pairs:
nb.addException(pair[0], pair[1], pair[2], pair[3], pair[4], True) nb.addException(pair[0], pair[1], pair[2], pair[3], pair[4], True)
...@@ -1122,7 +1199,7 @@ class GromacsTopFile(object): ...@@ -1122,7 +1199,7 @@ class GromacsTopFile(object):
if switchDistance is not None: if switchDistance is not None:
nb.setUseSwitchingFunction(True) nb.setUseSwitchingFunction(True)
nb.setSwitchingDistance(switchDistance) nb.setSwitchingDistance(switchDistance)
if self._defaults[1] in ('1', '3'): if lj is not None:
methodMap = {ff.NoCutoff:mm.CustomNonbondedForce.NoCutoff, methodMap = {ff.NoCutoff:mm.CustomNonbondedForce.NoCutoff,
ff.CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic, ff.CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic, ff.CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic,
...@@ -1131,14 +1208,14 @@ class GromacsTopFile(object): ...@@ -1131,14 +1208,14 @@ class GromacsTopFile(object):
ff.LJPME:mm.CustomNonbondedForce.CutoffPeriodic} ff.LJPME:mm.CustomNonbondedForce.CutoffPeriodic}
lj.setNonbondedMethod(methodMap[nonbondedMethod]) lj.setNonbondedMethod(methodMap[nonbondedMethod])
lj.setCutoffDistance(nonbondedCutoff) lj.setCutoffDistance(nonbondedCutoff)
if nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic):
lj.setUseLongRangeCorrection(True)
if switchDistance is not None: if switchDistance is not None:
lj.setUseSwitchingFunction(True) lj.setUseSwitchingFunction(True)
lj.setSwitchingDistance(switchDistance) lj.setSwitchingDistance(switchDistance)
lj.setName('LennardJonesForce')
if has_nbfix_terms: if has_nbfix_terms:
if self._defaults[1] != '2':
raise NotImplementedError('NBFIX terms with LB combination rule is not yet supported')
atom_nbfix_types = set([]) atom_nbfix_types = set([])
for pair in self._nonbondTypes: for pair in self._nonbondTypes:
atom_nbfix_types.add(pair[0]) atom_nbfix_types.add(pair[0])
...@@ -1146,30 +1223,26 @@ class GromacsTopFile(object): ...@@ -1146,30 +1223,26 @@ class GromacsTopFile(object):
lj_idx_list = [0 for _ in atom_types] lj_idx_list = [0 for _ in atom_types]
lj_radii, lj_depths = [], [] lj_radii, lj_depths = [], []
atom_params = []
num_lj_types = 0 num_lj_types = 0
lj_type_list = [] lj_type_list = []
for i,atom_type in enumerate(atom_types): for i,atom_type in enumerate(atom_types):
atom = self._atomTypes[atom_type] atom = self._atomTypes[atom_type]
if lj_idx_list[i]: continue # already assigned if lj_idx_list[i]: continue # already assigned
atom_rmin = atom[6] ljtype = (float(atom[6]), float(atom[7]))
atom_epsilon = atom[7] atom_params.append(ljtype)
num_lj_types += 1 num_lj_types += 1
lj_idx_list[i] = num_lj_types lj_idx_list[i] = num_lj_types
ljtype = (atom_rmin, atom_epsilon)
lj_type_list.append(atom) lj_type_list.append(atom)
lj_radii.append(float(atom_rmin))
lj_depths.append(float(atom_epsilon))
for j in range(i+1, len(atom_types)): for j in range(i+1, len(atom_types)):
atom_type2 = atom_types[j] atom_type2 = atom_types[j]
if lj_idx_list[j] > 0: continue # already assigned if lj_idx_list[j] > 0: continue # already assigned
atom2 = self._atomTypes[atom_type2] atom2 = self._atomTypes[atom_type2]
atom2_rmin = atom2[6] ljtype2 = (float(atom2[6]), float(atom2[7]))
atom2_epsilon = atom2[7]
if atom2 is atom: if atom2 is atom:
lj_idx_list[j] = num_lj_types lj_idx_list[j] = num_lj_types
elif atom_type not in atom_nbfix_types: elif atom_type not in atom_nbfix_types:
# Only non-NBFIXed atom types can be compressed # Only non-NBFIXed atom types can be compressed
ljtype2 = (atom2_rmin, atom2_epsilon)
if ljtype == ljtype2: if ljtype == ljtype2:
lj_idx_list[j] = num_lj_types lj_idx_list[j] = num_lj_types
...@@ -1182,43 +1255,34 @@ class GromacsTopFile(object): ...@@ -1182,43 +1255,34 @@ class GromacsTopFile(object):
for j in range(num_lj_types): for j in range(num_lj_types):
namej = lj_type_list[j][0] namej = lj_type_list[j][0]
try: try:
params = self._nonbondTypes[tuple(sorted((namei, namej)))] types = self._nonbondTypes[tuple(sorted((namei, namej)))]
rij = float(params[3]) params = (float(types[3]), float(types[4]))
wdij = float(params[4]) if self._defaults[1] == '2':
c6 = 4 * params[1] * params[0]**6
c12 = 4 * params[1] * params[0]**12
else:
c6 = params[0]
c12 = params[1]
except KeyError: except KeyError:
rij = (lj_radii[i] + lj_radii[j]) / 2 params1 = atom_params[i]
wdij = math.sqrt(lj_depths[i] * lj_depths[j]) params2 = atom_params[j]
acoef[i+num_lj_types*j] = 2 * math.sqrt(wdij) * rij**6 if self._defaults[1] == '1':
bcoef[i+num_lj_types*j] = 4 * wdij * rij**6 c6 = math.sqrt(params1[0]*params2[0])
cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6;' c12 = math.sqrt(params1[1]*params2[1])
'a=acoef(type1, type2);' else:
'b=bcoef(type1, type2)') if self._defaults[1] == '2':
cforce.addTabulatedFunction('acoef', sigma = (params1[0] + params2[0]) / 2
mm.Discrete2DFunction(num_lj_types, num_lj_types, acoef)) else:
cforce.addTabulatedFunction('bcoef', sigma = math.sqrt(params1[0] + params2[0])
mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef)) epsilon = math.sqrt(params1[1] * params2[1])
cforce.addPerParticleParameter('type') c6 = 4 * epsilon * sigma**6
if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)): c12 = 4 * epsilon * sigma**12
cforce.setNonbondedMethod(cforce.CutoffPeriodic) acoef[i+num_lj_types*j] = math.sqrt(c12)
cforce.setCutoffDistance(nonbondedCutoff) bcoef[i+num_lj_types*j] = c6
cforce.setUseLongRangeCorrection(True) lj.addTabulatedFunction('acoef', mm.Discrete2DFunction(num_lj_types, num_lj_types, acoef))
elif nonbondedMethod is ff.NoCutoff: lj.addTabulatedFunction('bcoef', mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef))
cforce.setNonbondedMethod(cforce.NoCutoff) for i, idx in enumerate(lj_idx_list):
elif nonbondedMethod is ff.CutoffNonPeriodic: lj.setParticleParameters(i, [idx-1]) # adjust for indexing from 0
cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
else:
raise ValueError('Unrecognized nonbonded method')
if switchDistance is not None:
cforce.setUseSwitchingFunction(True)
cforce.setSwitchingDistance(switchDistance)
for i in lj_idx_list:
cforce.addParticle((i - 1,)) # adjust for indexing from 0
for i in range(nb.getNumExceptions()):
ii, jj, q, eps, sig = nb.getExceptionParameters(i)
cforce.addExclusion(ii, jj)
sys.addForce(cforce)
# Adjust masses. # Adjust masses.
......
wrappers/python/tests/TestGromacsTopFile.py
View file @ 25f4e982
...@@ -5,6 +5,7 @@ from openmm import * ...@@ -5,6 +5,7 @@ from openmm import *
from openmm.unit import * from openmm.unit import *
from openmm.app.gromacstopfile import _defaultGromacsIncludeDir from openmm.app.gromacstopfile import _defaultGromacsIncludeDir
import openmm.app.element as elem import openmm.app.element as elem
from numpy.testing import assert_allclose
GROMACS_INCLUDE = _defaultGromacsIncludeDir() GROMACS_INCLUDE = _defaultGromacsIncludeDir()
...@@ -227,6 +228,32 @@ class TestGromacsTopFile(unittest.TestCase): ...@@ -227,6 +228,32 @@ class TestGromacsTopFile(unittest.TestCase):
self.assertAlmostEqual(0.106676721, vs.getWeight(1)) self.assertAlmostEqual(0.106676721, vs.getWeight(1))
self.assertAlmostEqual(0.106676721, vs.getWeight(2)) self.assertAlmostEqual(0.106676721, vs.getWeight(2))
def test_GROMOS(self):
"""Test a system using the GROMOS 54a7 force field."""
top = GromacsTopFile('systems/1ppt.top')
gro = GromacsGroFile('systems/1ppt.gro')
system = top.createSystem()
for i, f in enumerate(system.getForces()):
f.setForceGroup(i)
context = Context(system, VerletIntegrator(1*femtosecond), Platform.getPlatformByName('Reference'))
context.setPositions(gro.positions)
energy = {}
for i, f in enumerate(system.getForces()):
energy[f.getName()] = context.getState(getEnergy=True, groups={i}).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
# Compare to energies computed with GROMACS.
assert_allclose(1.12797e+03, energy['GROMOSBondForce'], rtol=1e-4)
assert_allclose(5.59066e+02, energy['GROMOSAngleForce'], rtol=1e-4)
assert_allclose(3.80152e+02, energy['PeriodicTorsionForce'], rtol=1e-4)
assert_allclose(9.59178e+01, energy['HarmonicTorsionForce'], rtol=1e-4)
assert_allclose(2.75307e+02, energy['LennardJonesExceptions'], rtol=1e-4)
assert_allclose(-7.53704e+02, energy['LennardJonesForce'], rtol=1e-4)
assert_allclose(-6.23055e+03+4.36880e+03, energy['NonbondedForce'], rtol=1e-4)
total = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
assert_allclose(-1.77020e+02, total, rtol=1e-3)
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/1ppt.gro 0 → 100644
View file @ 25f4e982
Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
391
1GLY N 1 0.230 -0.964 1.825
1GLY H1 2 0.296 -0.897 1.860
1GLY H2 3 0.172 -0.996 1.901
1GLY H3 4 0.278 -1.041 1.785
1GLY CA 5 0.147 -0.902 1.725
1GLY C 6 0.045 -0.998 1.670
1GLY O 7 0.021 -1.107 1.735
2PRO N 8 -0.017 -0.967 1.562
2PRO CA 9 -0.113 -1.061 1.496
2PRO CB 10 -0.172 -0.983 1.378
2PRO CG 11 -0.082 -0.868 1.355
2PRO CD 12 0.011 -0.845 1.478
2PRO C 13 -0.038 -1.182 1.449
2PRO O 14 0.078 -1.186 1.408
3SER N 15 -0.118 -1.292 1.457
3SER H 16 -0.211 -1.287 1.495
3SER CA 17 -0.063 -1.419 1.405
3SER CB 18 -0.136 -1.536 1.457
3SER OG 19 -0.266 -1.523 1.421
3SER HG 20 -0.317 -1.602 1.455
3SER C 21 -0.064 -1.419 1.249
3SER O 22 -0.115 -1.333 1.183
4GLN N 23 0.024 -1.500 1.196
4GLN H 24 0.075 -1.564 1.254
4GLN CA 25 0.049 -1.494 1.048
4GLN CB 26 0.164 -1.589 1.011
4GLN CG 27 0.218 -1.570 0.870
4GLN CD 28 0.331 -1.667 0.837
4GLN OE1 29 0.372 -1.676 0.721
4GLN NE2 30 0.386 -1.740 0.932
4GLN HE21 31 0.354 -1.732 1.026
4GLN HE22 32 0.460 -1.804 0.909
4GLN C 33 -0.077 -1.538 0.973
4GLN O 34 -0.133 -1.645 1.002
5PRO N 35 -0.120 -1.465 0.875
5PRO CA 36 -0.241 -1.497 0.809
5PRO CB 37 -0.280 -1.385 0.715
5PRO CG 38 -0.181 -1.275 0.744
5PRO CD 39 -0.077 -1.319 0.841
5PRO C 40 -0.226 -1.630 0.726
5PRO O 41 -0.118 -1.660 0.682
6THR N 42 -0.338 -1.692 0.717
6THR H 43 -0.417 -1.658 0.769
6THR CA 44 -0.355 -1.816 0.631
6THR CB 45 -0.475 -1.891 0.688
6THR OG1 46 -0.404 -1.950 0.807
6THR HG1 47 -0.468 -2.006 0.861
6THR CG2 48 -0.480 -2.026 0.606
6THR C 49 -0.375 -1.775 0.486
6THR O 50 -0.469 -1.704 0.452
7TYR N 51 -0.289 -1.821 0.395
7TYR H 52 -0.209 -1.871 0.427
7TYR CA 53 -0.306 -1.802 0.250
7TYR CB 54 -0.183 -1.859 0.179
7TYR CG 55 -0.191 -1.841 0.026
7TYR CD1 56 -0.203 -1.712 -0.028
7TYR HD1 57 -0.207 -1.633 0.032
7TYR CD2 58 -0.188 -1.952 -0.059
7TYR HD2 59 -0.182 -2.044 -0.020
7TYR CE1 60 -0.209 -1.695 -0.167
7TYR HE1 61 -0.217 -1.603 -0.206
7TYR CE2 62 -0.194 -1.934 -0.198
7TYR HE2 63 -0.192 -2.014 -0.258
7TYR CZ 64 -0.204 -1.806 -0.252
7TYR OH 65 -0.207 -1.788 -0.387
7TYR HH 66 -0.202 -1.876 -0.432
7TYR C 67 -0.433 -1.874 0.201
7TYR O 68 -0.454 -1.993 0.229
8PRO N 69 -0.526 -1.807 0.144
8PRO CA 70 -0.657 -1.863 0.100
8PRO CB 71 -0.749 -1.740 0.080
8PRO CG 72 -0.658 -1.631 0.043
8PRO CD 73 -0.523 -1.661 0.117
8PRO C 74 -0.649 -1.953 -0.019
8PRO O 75 -0.758 -2.024 -0.051
9GLY N 76 -0.538 -1.974 -0.086
9GLY H 77 -0.453 -1.926 -0.062
9GLY CA 78 -0.542 -2.073 -0.198
9GLY C 79 -0.526 -1.986 -0.321
9GLY O 80 -0.579 -1.878 -0.334
10ASP N 81 -0.463 -2.046 -0.425
10ASP H 82 -0.421 -2.136 -0.409
10ASP CA 83 -0.452 -1.987 -0.561
10ASP CB 84 -0.370 -2.077 -0.652
10ASP CG 85 -0.222 -2.089 -0.612
10ASP OD1 86 -0.152 -2.189 -0.654
10ASP OD2 87 -0.168 -2.001 -0.535
10ASP C 88 -0.589 -1.964 -0.623
10ASP O 89 -0.608 -1.870 -0.701
11ASP N 90 -0.681 -2.049 -0.592
11ASP H 91 -0.662 -2.120 -0.524
11ASP CA 92 -0.811 -2.041 -0.654
11ASP CB 93 -0.868 -2.181 -0.685
11ASP CG 94 -0.779 -2.257 -0.783
11ASP OD1 95 -0.740 -2.200 -0.891
11ASP OD2 96 -0.743 -2.378 -0.756
11ASP C 97 -0.914 -1.968 -0.569
11ASP O 98 -1.027 -1.945 -0.615
12ALA N 99 -0.861 -1.889 -0.477
12ALA H 100 -0.763 -1.881 -0.461
12ALA CA 101 -0.962 -1.813 -0.402
12ALA CB 102 -0.883 -1.758 -0.279
12ALA C 103 -1.010 -1.693 -0.482
12ALA O 104 -0.948 -1.647 -0.578
13PRO N 105 -1.137 -1.655 -0.469
13PRO CA 106 -1.198 -1.541 -0.547
13PRO CB 107 -1.342 -1.524 -0.491
13PRO CG 108 -1.350 -1.601 -0.366
13PRO CD 109 -1.224 -1.688 -0.348
13PRO C 110 -1.119 -1.412 -0.521
13PRO O 111 -1.052 -1.396 -0.403
14VAL N 112 -1.118 -1.319 -0.613
14VAL H 113 -1.172 -1.329 -0.696
14VAL CA 114 -1.034 -1.195 -0.591
14VAL CB 115 -1.048 -1.111 -0.716
14VAL CG1 116 -0.981 -0.975 -0.706
14VAL CG2 117 -1.001 -1.187 -0.843
14VAL C 118 -1.067 -1.123 -0.461
14VAL O 119 -0.973 -1.072 -0.390
15GLU N 120 -1.184 -1.132 -0.411
15GLU H 121 -1.254 -1.188 -0.455
15GLU CA 122 -1.214 -1.055 -0.285
15GLU CB 123 -1.371 -1.055 -0.259
15GLU CG 124 -1.421 -1.185 -0.196
15GLU CD 125 -1.556 -1.170 -0.125
15GLU OE1 126 -1.615 -1.273 -0.076
15GLU OE2 127 -1.611 -1.053 -0.116
15GLU C 128 -1.145 -1.117 -0.170
15GLU O 129 -1.117 -1.038 -0.076
16ASP N 130 -1.132 -1.250 -0.170
16ASP H 131 -1.180 -1.303 -0.239
16ASP CA 132 -1.049 -1.319 -0.072
16ASP CB 133 -1.071 -1.467 -0.064
16ASP CG 134 -1.211 -1.502 -0.015
16ASP OD1 135 -1.257 -1.621 -0.034
16ASP OD2 136 -1.282 -1.413 0.044
16ASP C 137 -0.900 -1.298 -0.096
16ASP O 138 -0.824 -1.284 0.001
17LEU N 139 -0.848 -1.279 -0.211
17LEU H 140 -0.901 -1.287 -0.295
17LEU CA 141 -0.703 -1.244 -0.213
17LEU CB 142 -0.665 -1.247 -0.363
17LEU CG 143 -0.652 -1.393 -0.406
17LEU CD1 144 -0.625 -1.392 -0.558
17LEU CD2 145 -0.537 -1.466 -0.326
17LEU C 146 -0.681 -1.098 -0.172
17LEU O 147 -0.581 -1.072 -0.116
18ILE N 148 -0.779 -1.008 -0.188
18ILE H 149 -0.862 -1.034 -0.236
18ILE CA 150 -0.768 -0.868 -0.135
18ILE CB 151 -0.882 -0.787 -0.196
18ILE CG1 152 -0.851 -0.756 -0.345
18ILE CG2 153 -0.897 -0.660 -0.112
18ILE CD 154 -0.964 -0.695 -0.412
18ILE C 155 -0.779 -0.875 0.018
18ILE O 156 -0.694 -0.810 0.082
19ARG N 157 -0.870 -0.954 0.077
19ARG H 158 -0.939 -1.004 0.024
19ARG CA 159 -0.864 -0.964 0.228
19ARG CB 160 -0.974 -1.058 0.260
19ARG CG 161 -1.101 -0.986 0.312
19ARG CD 162 -1.221 -1.074 0.360
19ARG NE 163 -1.324 -1.059 0.262
19ARG HE 164 -1.288 -1.079 0.171
19ARG CZ 165 -1.456 -1.026 0.252
19ARG NH1 166 -1.565 -0.993 0.345
19ARG HH11 167 -1.548 -0.992 0.444
19ARG HH12 168 -1.656 -0.972 0.310
19ARG NH2 169 -1.488 -1.017 0.133
19ARG HH21 170 -1.419 -1.033 0.062
19ARG HH22 171 -1.581 -0.993 0.108
19ARG C 172 -0.727 -1.018 0.272
19ARG O 173 -0.674 -0.980 0.377
20PHE N 174 -0.670 -1.122 0.213
20PHE H 175 -0.718 -1.165 0.136
20PHE CA 176 -0.544 -1.178 0.255
20PHE CB 177 -0.510 -1.297 0.165
20PHE CG 178 -0.371 -1.351 0.195
20PHE CD1 179 -0.267 -1.333 0.103
20PHE HD1 180 -0.283 -1.285 0.017
20PHE CD2 181 -0.349 -1.418 0.315
20PHE HD2 182 -0.424 -1.431 0.380
20PHE CE1 183 -0.139 -1.383 0.133
20PHE HE1 184 -0.064 -1.371 0.068
20PHE CE2 185 -0.222 -1.468 0.344
20PHE HE2 186 -0.206 -1.516 0.430
20PHE CZ 187 -0.117 -1.450 0.254
20PHE HZ 188 -0.026 -1.485 0.275
20PHE C 189 -0.437 -1.069 0.239
20PHE O 190 -0.349 -1.054 0.325
21TYR N 191 -0.435 -0.992 0.128
21TYR H 192 -0.505 -1.009 0.059
21TYR CA 193 -0.340 -0.888 0.101
21TYR CB 194 -0.382 -0.814 -0.027
21TYR CG 195 -0.306 -0.687 -0.056
21TYR CD1 196 -0.173 -0.692 -0.099
21TYR HD1 197 -0.128 -0.781 -0.112
21TYR CD2 198 -0.371 -0.565 -0.038
21TYR HD2 199 -0.466 -0.563 -0.007
21TYR CE1 200 -0.104 -0.573 -0.125
21TYR HE1 201 -0.009 -0.576 -0.156
21TYR CE2 202 -0.302 -0.447 -0.062
21TYR HE2 203 -0.348 -0.359 -0.049
21TYR CZ 204 -0.169 -0.451 -0.106
21TYR OH 205 -0.104 -0.333 -0.129
21TYR HH 206 -0.165 -0.257 -0.110
21TYR C 207 -0.341 -0.790 0.218
21TYR O 208 -0.236 -0.753 0.272
22ASP N 209 -0.464 -0.747 0.259
22ASP H 210 -0.547 -0.782 0.215
22ASP CA 211 -0.473 -0.647 0.369
22ASP CB 212 -0.619 -0.606 0.385
22ASP CG 213 -0.671 -0.516 0.275
22ASP OD1 214 -0.797 -0.512 0.249
22ASP OD2 215 -0.589 -0.443 0.207
22ASP C 216 -0.421 -0.709 0.498
22ASP O 217 -0.357 -0.640 0.578
23ASN N 218 -0.451 -0.839 0.527
23ASN H 219 -0.503 -0.894 0.463
23ASN CA 220 -0.404 -0.895 0.654
23ASN CB 221 -0.472 -1.025 0.686
23ASN CG 222 -0.619 -1.011 0.726
23ASN OD1 223 -0.684 -1.128 0.724
23ASN ND2 224 -0.669 -0.904 0.758
23ASN HD21 225 -0.614 -0.821 0.759
23ASN HD22 226 -0.766 -0.900 0.784
23ASN C 227 -0.251 -0.914 0.640
23ASN O 228 -0.184 -0.894 0.745
24LEU N 229 -0.199 -0.951 0.527
24LEU H 230 -0.256 -0.967 0.446
24LEU CA 231 -0.045 -0.968 0.521
24LEU CB 232 -0.020 -1.015 0.380
24LEU CG 233 0.128 -1.048 0.355
24LEU CD1 234 0.176 -1.147 0.454
24LEU CD2 235 0.150 -1.101 0.208
24LEU C 236 0.017 -0.827 0.543
24LEU O 237 0.122 -0.826 0.598
25GLN N 238 -0.041 -0.720 0.491
25GLN H 239 -0.124 -0.733 0.436
25GLN CA 240 0.009 -0.588 0.510
25GLN CB 241 -0.081 -0.483 0.443
25GLN CG 242 -0.028 -0.340 0.449
25GLN CD 243 -0.092 -0.250 0.342
25GLN OE1 244 -0.040 -0.143 0.313
25GLN NE2 245 -0.203 -0.289 0.281
25GLN HE21 246 -0.245 -0.376 0.304
25GLN HE22 247 -0.244 -0.230 0.212
25GLN C 248 0.019 -0.554 0.658
25GLN O 249 0.126 -0.515 0.706
26GLN N 250 -0.086 -0.575 0.731
26GLN H 251 -0.170 -0.605 0.686
26GLN CA 252 -0.086 -0.556 0.876
26GLN CB 253 -0.227 -0.587 0.930
26GLN CG 254 -0.236 -0.575 1.082
26GLN CD 255 -0.233 -0.430 1.131
26GLN OE1 256 -0.241 -0.405 1.252
26GLN NE2 257 -0.222 -0.331 1.044
26GLN HE21 258 -0.216 -0.351 0.947
26GLN HE22 259 -0.221 -0.236 1.076
26GLN C 260 0.031 -0.629 0.940
26GLN O 261 0.101 -0.592 1.027
27TYR N 262 0.037 -0.763 0.916
27TYR H 263 -0.033 -0.802 0.856
27TYR CA 264 0.136 -0.852 0.970
27TYR CB 265 0.111 -0.995 0.912
27TYR CG 266 0.212 -1.099 0.959
27TYR CD1 267 0.312 -1.144 0.873
27TYR HD1 268 0.317 -1.109 0.779
27TYR CD2 269 0.204 -1.148 1.090
27TYR HD2 270 0.132 -1.117 1.151
27TYR CE1 271 0.406 -1.238 0.917
27TYR HE1 272 0.478 -1.270 0.855
27TYR CE2 273 0.298 -1.242 1.135
27TYR HE2 274 0.293 -1.278 1.228
27TYR CZ 275 0.400 -1.286 1.049
27TYR OH 276 0.493 -1.375 1.092
27TYR HH 277 0.474 -1.399 1.187
27TYR C 278 0.276 -0.804 0.936
27TYR O 279 0.362 -0.794 1.025
28LEU N 280 0.305 -0.774 0.817
28LEU H 281 0.234 -0.782 0.747
28LEU CA 282 0.434 -0.728 0.778
28LEU CB 283 0.461 -0.714 0.631
28LEU CG 284 0.449 -0.851 0.556
28LEU CD1 285 0.443 -0.825 0.397
28LEU CD2 286 0.576 -0.936 0.584
28LEU C 287 0.468 -0.591 0.848
28LEU O 288 0.589 -0.581 0.893
29ASN N 289 0.374 -0.499 0.853
29ASN H 290 0.286 -0.511 0.807
29ASN CA 291 0.406 -0.373 0.933
29ASN CB 292 0.275 -0.289 0.939
29ASN CG 293 0.258 -0.213 0.808
29ASN OD1 294 0.156 -0.147 0.790
29ASN ND2 295 0.354 -0.220 0.717
29ASN HD21 296 0.436 -0.275 0.735
29ASN HD22 297 0.345 -0.170 0.631
29ASN C 298 0.450 -0.408 1.075
29ASN O 299 0.525 -0.332 1.138
30VAL N 300 0.381 -0.504 1.146
30VAL H 301 0.309 -0.555 1.098
30VAL CA 302 0.407 -0.535 1.282
30VAL CB 303 0.296 -0.625 1.346
30VAL CG1 304 0.353 -0.659 1.495
30VAL CG2 305 0.168 -0.544 1.367
30VAL C 306 0.538 -0.603 1.295
30VAL O 307 0.627 -0.568 1.383
31VAL N 308 0.570 -0.697 1.204
31VAL H 309 0.507 -0.717 1.128
31VAL CA 310 0.700 -0.770 1.216
31VAL CB 311 0.684 -0.881 1.098
31VAL CG1 312 0.822 -0.944 1.076
31VAL CG2 313 0.584 -0.991 1.134
31VAL C 314 0.816 -0.678 1.196
31VAL O 315 0.930 -0.700 1.240
32THR N 316 0.804 -0.585 1.102
32THR H 317 0.720 -0.583 1.047
32THR CA 318 0.907 -0.486 1.074
32THR CB 319 0.883 -0.434 0.934
32THR OG1 320 0.776 -0.357 0.906
32THR HG1 321 0.778 -0.332 0.809
32THR CG2 322 0.961 -0.485 0.844
32THR C 323 0.897 -0.362 1.169
32THR O 324 0.988 -0.275 1.152
33ARG N 325 0.815 -0.360 1.267
33ARG H 326 0.756 -0.440 1.278
33ARG CA 327 0.799 -0.250 1.366
33ARG CB 328 0.924 -0.238 1.456
33ARG CG 329 0.971 -0.373 1.507
33ARG CD 330 1.087 -0.361 1.604
33ARG NE 331 1.055 -0.281 1.722
33ARG HE 332 1.080 -0.184 1.722
33ARG CZ 333 0.994 -0.331 1.830
33ARG NH1 334 0.957 -0.460 1.835
33ARG HH11 335 0.976 -0.520 1.758
33ARG HH12 336 0.912 -0.496 1.917
33ARG NH2 337 0.965 -0.258 1.939
33ARG HH21 338 0.989 -0.161 1.943
33ARG HH22 339 0.919 -0.301 2.017
33ARG C 340 0.779 -0.117 1.294
33ARG O 341 0.804 -0.009 1.351
34HIS N 342 0.703 -0.123 1.190
34HIS H 343 0.662 -0.210 1.162
34HIS CA 344 0.678 0.004 1.110
34HIS CB 345 0.759 -0.001 0.988
34HIS CG 346 0.761 0.129 0.910
34HIS ND1 347 0.695 0.143 0.788
34HIS CD2 348 0.820 0.249 0.936
34HIS HD2 349 0.875 0.271 1.016
34HIS CE1 350 0.714 0.267 0.745
34HIS HE1 351 0.678 0.305 0.660
34HIS NE2 352 0.788 0.331 0.833
34HIS HE2 353 0.817 0.426 0.825
34HIS C 354 0.529 0.016 1.080
34HIS O 355 0.484 -0.014 0.969
35ARG N 356 0.452 0.054 1.188
35ARG H 357 0.499 0.078 1.273
35ARG CA 358 0.311 0.062 1.185
35ARG CB 359 0.255 0.064 1.331
35ARG CG 360 0.285 -0.071 1.399
35ARG CD 361 0.248 -0.079 1.548
35ARG NE 362 0.331 -0.175 1.622
35ARG HE 363 0.430 -0.162 1.619
35ARG CZ 364 0.284 -0.277 1.694
35ARG NH1 365 0.152 -0.301 1.704
35ARG HH11 366 0.087 -0.241 1.656
35ARG HH12 367 0.119 -0.378 1.758
35ARG NH2 368 0.361 -0.363 1.762
35ARG HH21 369 0.461 -0.353 1.761
35ARG HH22 370 0.320 -0.438 1.814
35ARG C 371 0.264 0.188 1.113
35ARG O 372 0.145 0.223 1.117
36TYR N 373 0.336 0.261 1.044
36TYR H 374 0.435 0.265 1.063
36TYR CA 375 0.276 0.345 0.930
36TYR CB 376 0.402 0.433 0.879
36TYR CG 377 0.473 0.479 1.006
36TYR CD1 378 0.567 0.396 1.068
36TYR HD1 379 0.588 0.306 1.030
36TYR CD2 380 0.442 0.604 1.062
36TYR HD2 381 0.373 0.662 1.019
36TYR CE1 382 0.633 0.439 1.184
36TYR HE1 383 0.701 0.380 1.228
36TYR CE2 384 0.508 0.647 1.177
36TYR HE2 385 0.487 0.736 1.217
36TYR CZ 386 0.604 0.565 1.238
36TYR OH 387 0.670 0.609 1.349
36TYR HH 388 0.638 0.700 1.373
36TYR C 389 0.233 0.248 0.820
36TYR O1 390 0.317 0.172 0.767
36TYR O2 391 0.128 0.214 0.789
10 10 10 0.00000 0.00000 0.00000 0.00000 -0.74749 0.00000
wrappers/python/tests/systems/1ppt.top 0 → 100644
View file @ 25f4e982
;
; File 'topol.top' was generated
; By user: peastman (1000)
; On host: System76
; At date: Tue Apr 4 11:57:56 2023
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2022.3-conda_forge (-:
;
; Executable: /home/peastman/miniconda3/envs/cf/bin.AVX2_256/gmx
; Data prefix: /home/peastman/miniconda3/envs/cf
; Working dir: /home/peastman/temp4
; Command line:
; gmx pdb2gmx -f 1ppt-fixed.pdb
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "gromos54a7.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 GLY rtp GLY q +1.0
1 NL 1 GLY N 1 0.129 14.0067
2 H 1 GLY H1 1 0.248 1.008
3 H 1 GLY H2 1 0.248 1.008
4 H 1 GLY H3 1 0.248 1.008
5 CH2 1 GLY CA 2 0.127 14.027
6 C 1 GLY C 3 0.45 12.011
7 O 1 GLY O 3 -0.45 15.9994 ; qtot 1
; residue 2 PRO rtp PRO q 0.0
8 N 2 PRO N 4 0 14.0067
9 CH1 2 PRO CA 5 0 13.019
10 CH2r 2 PRO CB 5 0 14.027
11 CH2r 2 PRO CG 6 0 14.027
12 CH2r 2 PRO CD 6 0 14.027
13 C 2 PRO C 7 0.45 12.011
14 O 2 PRO O 7 -0.45 15.9994 ; qtot 1
; residue 3 SER rtp SER q 0.0
15 N 3 SER N 8 -0.31 14.0067
16 H 3 SER H 8 0.31 1.008
17 CH1 3 SER CA 9 0 13.019
18 CH2 3 SER CB 10 0.266 14.027
19 OA 3 SER OG 10 -0.674 15.9994
20 H 3 SER HG 10 0.408 1.008
21 C 3 SER C 11 0.45 12.011
22 O 3 SER O 11 -0.45 15.9994 ; qtot 1
; residue 4 GLN rtp GLN q 0.0
23 N 4 GLN N 12 -0.31 14.0067
24 H 4 GLN H 12 0.31 1.008
25 CH1 4 GLN CA 13 0 13.019
26 CH2 4 GLN CB 13 0 14.027
27 CH2 4 GLN CG 13 0 14.027
28 C 4 GLN CD 14 0.29 12.011
29 O 4 GLN OE1 14 -0.45 15.9994
30 NT 4 GLN NE2 14 -0.72 14.0067
31 H 4 GLN HE21 14 0.44 1.008
32 H 4 GLN HE22 14 0.44 1.008
33 C 4 GLN C 15 0.45 12.011
34 O 4 GLN O 15 -0.45 15.9994 ; qtot 1
; residue 5 PRO rtp PRO q 0.0
35 N 5 PRO N 16 0 14.0067
36 CH1 5 PRO CA 17 0 13.019
37 CH2r 5 PRO CB 17 0 14.027
38 CH2r 5 PRO CG 18 0 14.027
39 CH2r 5 PRO CD 18 0 14.027
40 C 5 PRO C 19 0.45 12.011
41 O 5 PRO O 19 -0.45 15.9994 ; qtot 1
; residue 6 THR rtp THR q 0.0
42 N 6 THR N 20 -0.31 14.0067
43 H 6 THR H 20 0.31 1.008
44 CH1 6 THR CA 21 0 13.019
45 CH1 6 THR CB 22 0.266 13.019
46 OA 6 THR OG1 22 -0.674 15.9994
47 H 6 THR HG1 22 0.408 1.008
48 CH3 6 THR CG2 23 0 15.035
49 C 6 THR C 24 0.45 12.011
50 O 6 THR O 24 -0.45 15.9994 ; qtot 1
; residue 7 TYR rtp TYR q 0.0
51 N 7 TYR N 25 -0.31 14.0067
52 H 7 TYR H 25 0.31 1.008
53 CH1 7 TYR CA 26 0 13.019
54 CH2 7 TYR CB 26 0 14.027
55 C 7 TYR CG 26 0 12.011
56 C 7 TYR CD1 27 -0.14 12.011
57 HC 7 TYR HD1 27 0.14 1.008
58 C 7 TYR CD2 28 -0.14 12.011
59 HC 7 TYR HD2 28 0.14 1.008
60 C 7 TYR CE1 29 -0.14 12.011
61 HC 7 TYR HE1 29 0.14 1.008
62 C 7 TYR CE2 30 -0.14 12.011
63 HC 7 TYR HE2 30 0.14 1.008
64 C 7 TYR CZ 31 0.203 12.011
65 OA 7 TYR OH 31 -0.611 15.9994
66 H 7 TYR HH 31 0.408 1.008
67 C 7 TYR C 32 0.45 12.011
68 O 7 TYR O 32 -0.45 15.9994 ; qtot 1
; residue 8 PRO rtp PRO q 0.0
69 N 8 PRO N 33 0 14.0067
70 CH1 8 PRO CA 34 0 13.019
71 CH2r 8 PRO CB 34 0 14.027
72 CH2r 8 PRO CG 35 0 14.027
73 CH2r 8 PRO CD 35 0 14.027
74 C 8 PRO C 36 0.45 12.011
75 O 8 PRO O 36 -0.45 15.9994 ; qtot 1
; residue 9 GLY rtp GLY q 0.0
76 N 9 GLY N 37 -0.31 14.0067
77 H 9 GLY H 37 0.31 1.008
78 CH2 9 GLY CA 38 0 14.027
79 C 9 GLY C 39 0.45 12.011
80 O 9 GLY O 39 -0.45 15.9994 ; qtot 1
; residue 10 ASP rtp ASP q -1.0
81 N 10 ASP N 40 -0.31 14.0067
82 H 10 ASP H 40 0.31 1.008
83 CH1 10 ASP CA 41 0 13.019
84 CH2 10 ASP CB 41 0 14.027
85 C 10 ASP CG 42 0.27 12.011
86 OM 10 ASP OD1 42 -0.635 15.9994
87 OM 10 ASP OD2 42 -0.635 15.9994
88 C 10 ASP C 43 0.45 12.011
89 O 10 ASP O 43 -0.45 15.9994 ; qtot 0
; residue 11 ASP rtp ASP q -1.0
90 N 11 ASP N 44 -0.31 14.0067
91 H 11 ASP H 44 0.31 1.008
92 CH1 11 ASP CA 45 0 13.019
93 CH2 11 ASP CB 45 0 14.027
94 C 11 ASP CG 46 0.27 12.011
95 OM 11 ASP OD1 46 -0.635 15.9994
96 OM 11 ASP OD2 46 -0.635 15.9994
97 C 11 ASP C 47 0.45 12.011
98 O 11 ASP O 47 -0.45 15.9994 ; qtot -1
; residue 12 ALA rtp ALA q 0.0
99 N 12 ALA N 48 -0.31 14.0067
100 H 12 ALA H 48 0.31 1.008
101 CH1 12 ALA CA 49 0 13.019
102 CH3 12 ALA CB 49 0 15.035
103 C 12 ALA C 50 0.45 12.011
104 O 12 ALA O 50 -0.45 15.9994 ; qtot -1
; residue 13 PRO rtp PRO q 0.0
105 N 13 PRO N 51 0 14.0067
106 CH1 13 PRO CA 52 0 13.019
107 CH2r 13 PRO CB 52 0 14.027
108 CH2r 13 PRO CG 53 0 14.027
109 CH2r 13 PRO CD 53 0 14.027
110 C 13 PRO C 54 0.45 12.011
111 O 13 PRO O 54 -0.45 15.9994 ; qtot -1
; residue 14 VAL rtp VAL q 0.0
112 N 14 VAL N 55 -0.31 14.0067
113 H 14 VAL H 55 0.31 1.008
114 CH1 14 VAL CA 56 0 13.019
115 CH1 14 VAL CB 56 0 13.019
116 CH3 14 VAL CG1 56 0 15.035
117 CH3 14 VAL CG2 56 0 15.035
118 C 14 VAL C 57 0.45 12.011
119 O 14 VAL O 57 -0.45 15.9994 ; qtot -1
; residue 15 GLU rtp GLU q -1.0
120 N 15 GLU N 58 -0.31 14.0067
121 H 15 GLU H 58 0.31 1.008
122 CH1 15 GLU CA 59 0 13.019
123 CH2 15 GLU CB 59 0 14.027
124 CH2 15 GLU CG 59 0 14.027
125 C 15 GLU CD 60 0.27 12.011
126 OM 15 GLU OE1 60 -0.635 15.9994
127 OM 15 GLU OE2 60 -0.635 15.9994
128 C 15 GLU C 61 0.45 12.011
129 O 15 GLU O 61 -0.45 15.9994 ; qtot -2
; residue 16 ASP rtp ASP q -1.0
130 N 16 ASP N 62 -0.31 14.0067
131 H 16 ASP H 62 0.31 1.008
132 CH1 16 ASP CA 63 0 13.019
133 CH2 16 ASP CB 63 0 14.027
134 C 16 ASP CG 64 0.27 12.011
135 OM 16 ASP OD1 64 -0.635 15.9994
136 OM 16 ASP OD2 64 -0.635 15.9994
137 C 16 ASP C 65 0.45 12.011
138 O 16 ASP O 65 -0.45 15.9994 ; qtot -3
; residue 17 LEU rtp LEU q 0.0
139 N 17 LEU N 66 -0.31 14.0067
140 H 17 LEU H 66 0.31 1.008
141 CH1 17 LEU CA 67 0 13.019
142 CH2 17 LEU CB 67 0 14.027
143 CH1 17 LEU CG 68 0 13.019
144 CH3 17 LEU CD1 68 0 15.035
145 CH3 17 LEU CD2 68 0 15.035
146 C 17 LEU C 69 0.45 12.011
147 O 17 LEU O 69 -0.45 15.9994 ; qtot -3
; residue 18 ILE rtp ILE q 0.0
148 N 18 ILE N 70 -0.31 14.0067
149 H 18 ILE H 70 0.31 1.008
150 CH1 18 ILE CA 71 0 13.019
151 CH1 18 ILE CB 72 0 13.019
152 CH2 18 ILE CG1 72 0 14.027
153 CH3 18 ILE CG2 72 0 15.035
154 CH3 18 ILE CD 72 0 15.035
155 C 18 ILE C 73 0.45 12.011
156 O 18 ILE O 73 -0.45 15.9994 ; qtot -3
; residue 19 ARG rtp ARG q +1.0
157 N 19 ARG N 74 -0.31 14.0067
158 H 19 ARG H 74 0.31 1.008
159 CH1 19 ARG CA 75 0 13.019
160 CH2 19 ARG CB 75 0 14.027
161 CH2 19 ARG CG 75 0 14.027
162 CH2 19 ARG CD 76 0.09 14.027
163 NE 19 ARG NE 76 -0.11 14.0067
164 H 19 ARG HE 76 0.24 1.008
165 C 19 ARG CZ 76 0.34 12.011
166 NZ 19 ARG NH1 76 -0.26 14.0067
167 H 19 ARG HH11 76 0.24 1.008
168 H 19 ARG HH12 76 0.24 1.008
169 NZ 19 ARG NH2 76 -0.26 14.0067
170 H 19 ARG HH21 76 0.24 1.008
171 H 19 ARG HH22 76 0.24 1.008
172 C 19 ARG C 77 0.45 12.011
173 O 19 ARG O 77 -0.45 15.9994 ; qtot -2
; residue 20 PHE rtp PHE q 0.0
174 N 20 PHE N 78 -0.31 14.0067
175 H 20 PHE H 78 0.31 1.008
176 CH1 20 PHE CA 79 0 13.019
177 CH2 20 PHE CB 79 0 14.027
178 C 20 PHE CG 79 0 12.011
179 C 20 PHE CD1 80 -0.14 12.011
180 HC 20 PHE HD1 80 0.14 1.008
181 C 20 PHE CD2 81 -0.14 12.011
182 HC 20 PHE HD2 81 0.14 1.008
183 C 20 PHE CE1 82 -0.14 12.011
184 HC 20 PHE HE1 82 0.14 1.008
185 C 20 PHE CE2 83 -0.14 12.011
186 HC 20 PHE HE2 83 0.14 1.008
187 C 20 PHE CZ 84 -0.14 12.011
188 HC 20 PHE HZ 84 0.14 1.008
189 C 20 PHE C 85 0.45 12.011
190 O 20 PHE O 85 -0.45 15.9994 ; qtot -2
; residue 21 TYR rtp TYR q 0.0
191 N 21 TYR N 86 -0.31 14.0067
192 H 21 TYR H 86 0.31 1.008
193 CH1 21 TYR CA 87 0 13.019
194 CH2 21 TYR CB 87 0 14.027
195 C 21 TYR CG 87 0 12.011
196 C 21 TYR CD1 88 -0.14 12.011
197 HC 21 TYR HD1 88 0.14 1.008
198 C 21 TYR CD2 89 -0.14 12.011
199 HC 21 TYR HD2 89 0.14 1.008
200 C 21 TYR CE1 90 -0.14 12.011
201 HC 21 TYR HE1 90 0.14 1.008
202 C 21 TYR CE2 91 -0.14 12.011
203 HC 21 TYR HE2 91 0.14 1.008
204 C 21 TYR CZ 92 0.203 12.011
205 OA 21 TYR OH 92 -0.611 15.9994
206 H 21 TYR HH 92 0.408 1.008
207 C 21 TYR C 93 0.45 12.011
208 O 21 TYR O 93 -0.45 15.9994 ; qtot -2
; residue 22 ASP rtp ASP q -1.0
209 N 22 ASP N 94 -0.31 14.0067
210 H 22 ASP H 94 0.31 1.008
211 CH1 22 ASP CA 95 0 13.019
212 CH2 22 ASP CB 95 0 14.027
213 C 22 ASP CG 96 0.27 12.011
214 OM 22 ASP OD1 96 -0.635 15.9994
215 OM 22 ASP OD2 96 -0.635 15.9994
216 C 22 ASP C 97 0.45 12.011
217 O 22 ASP O 97 -0.45 15.9994 ; qtot -3
; residue 23 ASN rtp ASN q 0.0
218 N 23 ASN N 98 -0.31 14.0067
219 H 23 ASN H 98 0.31 1.008
220 CH1 23 ASN CA 99 0 13.019
221 CH2 23 ASN CB 99 0 14.027
222 C 23 ASN CG 100 0.29 12.011
223 O 23 ASN OD1 100 -0.45 15.9994
224 NT 23 ASN ND2 100 -0.72 14.0067
225 H 23 ASN HD21 100 0.44 1.008
226 H 23 ASN HD22 100 0.44 1.008
227 C 23 ASN C 101 0.45 12.011
228 O 23 ASN O 101 -0.45 15.9994 ; qtot -3
; residue 24 LEU rtp LEU q 0.0
229 N 24 LEU N 102 -0.31 14.0067
230 H 24 LEU H 102 0.31 1.008
231 CH1 24 LEU CA 103 0 13.019
232 CH2 24 LEU CB 103 0 14.027
233 CH1 24 LEU CG 104 0 13.019
234 CH3 24 LEU CD1 104 0 15.035
235 CH3 24 LEU CD2 104 0 15.035
236 C 24 LEU C 105 0.45 12.011
237 O 24 LEU O 105 -0.45 15.9994 ; qtot -3
; residue 25 GLN rtp GLN q 0.0
238 N 25 GLN N 106 -0.31 14.0067
239 H 25 GLN H 106 0.31 1.008
240 CH1 25 GLN CA 107 0 13.019
241 CH2 25 GLN CB 107 0 14.027
242 CH2 25 GLN CG 107 0 14.027
243 C 25 GLN CD 108 0.29 12.011
244 O 25 GLN OE1 108 -0.45 15.9994
245 NT 25 GLN NE2 108 -0.72 14.0067
246 H 25 GLN HE21 108 0.44 1.008
247 H 25 GLN HE22 108 0.44 1.008
248 C 25 GLN C 109 0.45 12.011
249 O 25 GLN O 109 -0.45 15.9994 ; qtot -3
; residue 26 GLN rtp GLN q 0.0
250 N 26 GLN N 110 -0.31 14.0067
251 H 26 GLN H 110 0.31 1.008
252 CH1 26 GLN CA 111 0 13.019
253 CH2 26 GLN CB 111 0 14.027
254 CH2 26 GLN CG 111 0 14.027
255 C 26 GLN CD 112 0.29 12.011
256 O 26 GLN OE1 112 -0.45 15.9994
257 NT 26 GLN NE2 112 -0.72 14.0067
258 H 26 GLN HE21 112 0.44 1.008
259 H 26 GLN HE22 112 0.44 1.008
260 C 26 GLN C 113 0.45 12.011
261 O 26 GLN O 113 -0.45 15.9994 ; qtot -3
; residue 27 TYR rtp TYR q 0.0
262 N 27 TYR N 114 -0.31 14.0067
263 H 27 TYR H 114 0.31 1.008
264 CH1 27 TYR CA 115 0 13.019
265 CH2 27 TYR CB 115 0 14.027
266 C 27 TYR CG 115 0 12.011
267 C 27 TYR CD1 116 -0.14 12.011
268 HC 27 TYR HD1 116 0.14 1.008
269 C 27 TYR CD2 117 -0.14 12.011
270 HC 27 TYR HD2 117 0.14 1.008
271 C 27 TYR CE1 118 -0.14 12.011
272 HC 27 TYR HE1 118 0.14 1.008
273 C 27 TYR CE2 119 -0.14 12.011
274 HC 27 TYR HE2 119 0.14 1.008
275 C 27 TYR CZ 120 0.203 12.011
276 OA 27 TYR OH 120 -0.611 15.9994
277 H 27 TYR HH 120 0.408 1.008
278 C 27 TYR C 121 0.45 12.011
279 O 27 TYR O 121 -0.45 15.9994 ; qtot -3
; residue 28 LEU rtp LEU q 0.0
280 N 28 LEU N 122 -0.31 14.0067
281 H 28 LEU H 122 0.31 1.008
282 CH1 28 LEU CA 123 0 13.019
283 CH2 28 LEU CB 123 0 14.027
284 CH1 28 LEU CG 124 0 13.019
285 CH3 28 LEU CD1 124 0 15.035
286 CH3 28 LEU CD2 124 0 15.035
287 C 28 LEU C 125 0.45 12.011
288 O 28 LEU O 125 -0.45 15.9994 ; qtot -3
; residue 29 ASN rtp ASN q 0.0
289 N 29 ASN N 126 -0.31 14.0067
290 H 29 ASN H 126 0.31 1.008
291 CH1 29 ASN CA 127 0 13.019
292 CH2 29 ASN CB 127 0 14.027
293 C 29 ASN CG 128 0.29 12.011
294 O 29 ASN OD1 128 -0.45 15.9994
295 NT 29 ASN ND2 128 -0.72 14.0067
296 H 29 ASN HD21 128 0.44 1.008
297 H 29 ASN HD22 128 0.44 1.008
298 C 29 ASN C 129 0.45 12.011
299 O 29 ASN O 129 -0.45 15.9994 ; qtot -3
; residue 30 VAL rtp VAL q 0.0
300 N 30 VAL N 130 -0.31 14.0067
301 H 30 VAL H 130 0.31 1.008
302 CH1 30 VAL CA 131 0 13.019
303 CH1 30 VAL CB 131 0 13.019
304 CH3 30 VAL CG1 131 0 15.035
305 CH3 30 VAL CG2 131 0 15.035
306 C 30 VAL C 132 0.45 12.011
307 O 30 VAL O 132 -0.45 15.9994 ; qtot -3
; residue 31 VAL rtp VAL q 0.0
308 N 31 VAL N 133 -0.31 14.0067
309 H 31 VAL H 133 0.31 1.008
310 CH1 31 VAL CA 134 0 13.019
311 CH1 31 VAL CB 134 0 13.019
312 CH3 31 VAL CG1 134 0 15.035
313 CH3 31 VAL CG2 134 0 15.035
314 C 31 VAL C 135 0.45 12.011
315 O 31 VAL O 135 -0.45 15.9994 ; qtot -3
; residue 32 THR rtp THR q 0.0
316 N 32 THR N 136 -0.31 14.0067
317 H 32 THR H 136 0.31 1.008
318 CH1 32 THR CA 137 0 13.019
319 CH1 32 THR CB 138 0.266 13.019
320 OA 32 THR OG1 138 -0.674 15.9994
321 H 32 THR HG1 138 0.408 1.008
322 CH3 32 THR CG2 139 0 15.035
323 C 32 THR C 140 0.45 12.011
324 O 32 THR O 140 -0.45 15.9994 ; qtot -3
; residue 33 ARG rtp ARG q +1.0
325 N 33 ARG N 141 -0.31 14.0067
326 H 33 ARG H 141 0.31 1.008
327 CH1 33 ARG CA 142 0 13.019
328 CH2 33 ARG CB 142 0 14.027
329 CH2 33 ARG CG 142 0 14.027
330 CH2 33 ARG CD 143 0.09 14.027
331 NE 33 ARG NE 143 -0.11 14.0067
332 H 33 ARG HE 143 0.24 1.008
333 C 33 ARG CZ 143 0.34 12.011
334 NZ 33 ARG NH1 143 -0.26 14.0067
335 H 33 ARG HH11 143 0.24 1.008
336 H 33 ARG HH12 143 0.24 1.008
337 NZ 33 ARG NH2 143 -0.26 14.0067
338 H 33 ARG HH21 143 0.24 1.008
339 H 33 ARG HH22 143 0.24 1.008
340 C 33 ARG C 144 0.45 12.011
341 O 33 ARG O 144 -0.45 15.9994 ; qtot -2
; residue 34 HIS rtp HISB q 0.0
342 N 34 HIS N 145 -0.31 14.0067
343 H 34 HIS H 145 0.31 1.008
344 CH1 34 HIS CA 146 0 13.019
345 CH2 34 HIS CB 146 0 14.027
346 C 34 HIS CG 147 0 12.011
347 NR 34 HIS ND1 147 -0.54 14.0067
348 C 34 HIS CD2 147 0 12.011
349 HC 34 HIS HD2 147 0.14 1.008
350 C 34 HIS CE1 147 0 12.011
351 HC 34 HIS HE1 147 0.14 1.008
352 NR 34 HIS NE2 147 -0.05 14.0067
353 H 34 HIS HE2 147 0.31 1.008
354 C 34 HIS C 148 0.45 12.011
355 O 34 HIS O 148 -0.45 15.9994 ; qtot -2
; residue 35 ARG rtp ARG q +1.0
356 N 35 ARG N 149 -0.31 14.0067
357 H 35 ARG H 149 0.31 1.008
358 CH1 35 ARG CA 150 0 13.019
359 CH2 35 ARG CB 150 0 14.027
360 CH2 35 ARG CG 150 0 14.027
361 CH2 35 ARG CD 151 0.09 14.027
362 NE 35 ARG NE 151 -0.11 14.0067
363 H 35 ARG HE 151 0.24 1.008
364 C 35 ARG CZ 151 0.34 12.011
365 NZ 35 ARG NH1 151 -0.26 14.0067
366 H 35 ARG HH11 151 0.24 1.008
367 H 35 ARG HH12 151 0.24 1.008
368 NZ 35 ARG NH2 151 -0.26 14.0067
369 H 35 ARG HH21 151 0.24 1.008
370 H 35 ARG HH22 151 0.24 1.008
371 C 35 ARG C 152 0.45 12.011
372 O 35 ARG O 152 -0.45 15.9994 ; qtot -1
; residue 36 TYR rtp TYR q -1.0
373 N 36 TYR N 153 -0.31 14.0067
374 H 36 TYR H 153 0.31 1.008
375 CH1 36 TYR CA 154 0 13.019
376 CH2 36 TYR CB 154 0 14.027
377 C 36 TYR CG 154 0 12.011
378 C 36 TYR CD1 155 -0.14 12.011
379 HC 36 TYR HD1 155 0.14 1.008
380 C 36 TYR CD2 156 -0.14 12.011
381 HC 36 TYR HD2 156 0.14 1.008
382 C 36 TYR CE1 157 -0.14 12.011
383 HC 36 TYR HE1 157 0.14 1.008
384 C 36 TYR CE2 158 -0.14 12.011
385 HC 36 TYR HE2 158 0.14 1.008
386 C 36 TYR CZ 159 0.203 12.011
387 OA 36 TYR OH 159 -0.611 15.9994
388 H 36 TYR HH 159 0.408 1.008
389 C 36 TYR C 160 0.27 12.011
390 OM 36 TYR O1 160 -0.635 15.9994
391 OM 36 TYR O2 160 -0.635 15.9994 ; qtot -2
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2
1 3 2 gb_2
1 4 2 gb_2
1 5 2 gb_21
5 6 2 gb_27
6 7 2 gb_5
6 8 2 gb_10
8 9 2 gb_21
8 12 2 gb_21
9 10 2 gb_27
9 13 2 gb_27
10 11 2 gb_27
11 12 2 gb_27
13 14 2 gb_5
13 15 2 gb_10
15 16 2 gb_2
15 17 2 gb_21
17 18 2 gb_27
17 21 2 gb_27
18 19 2 gb_18
19 20 2 gb_1
21 22 2 gb_5
21 23 2 gb_10
23 24 2 gb_2
23 25 2 gb_21
25 26 2 gb_27
25 33 2 gb_27
26 27 2 gb_27
27 28 2 gb_27
28 29 2 gb_5
28 30 2 gb_9
30 31 2 gb_2
30 32 2 gb_2
33 34 2 gb_5
33 35 2 gb_10
35 36 2 gb_21
35 39 2 gb_21
36 37 2 gb_27
36 40 2 gb_27
37 38 2 gb_27
38 39 2 gb_27
40 41 2 gb_5
40 42 2 gb_10
42 43 2 gb_2
42 44 2 gb_21
44 45 2 gb_27
44 49 2 gb_27
45 46 2 gb_18
45 48 2 gb_27
46 47 2 gb_1
49 50 2 gb_5
49 51 2 gb_10
51 52 2 gb_2
51 53 2 gb_21
53 54 2 gb_27
53 67 2 gb_27
54 55 2 gb_27
55 56 2 gb_16
55 58 2 gb_16
56 57 2 gb_3
56 60 2 gb_16
58 59 2 gb_3
58 62 2 gb_16
60 61 2 gb_3
60 64 2 gb_16
62 63 2 gb_3
62 64 2 gb_16
64 65 2 gb_13
65 66 2 gb_1
67 68 2 gb_5
67 69 2 gb_10
69 70 2 gb_21
69 73 2 gb_21
70 71 2 gb_27
70 74 2 gb_27
71 72 2 gb_27
72 73 2 gb_27
74 75 2 gb_5
74 76 2 gb_10
76 77 2 gb_2
76 78 2 gb_21
78 79 2 gb_27
79 80 2 gb_5
79 81 2 gb_10
81 82 2 gb_2
81 83 2 gb_21
83 84 2 gb_27
83 88 2 gb_27
84 85 2 gb_27
85 86 2 gb_6
85 87 2 gb_6
88 89 2 gb_5
88 90 2 gb_10
90 91 2 gb_2
90 92 2 gb_21
92 93 2 gb_27
92 97 2 gb_27
93 94 2 gb_27
94 95 2 gb_6
94 96 2 gb_6
97 98 2 gb_5
97 99 2 gb_10
99 100 2 gb_2
99 101 2 gb_21
101 102 2 gb_27
101 103 2 gb_27
103 104 2 gb_5
103 105 2 gb_10
105 106 2 gb_21
105 109 2 gb_21
106 107 2 gb_27
106 110 2 gb_27
107 108 2 gb_27
108 109 2 gb_27
110 111 2 gb_5
110 112 2 gb_10
112 113 2 gb_2
112 114 2 gb_21
114 115 2 gb_27
114 118 2 gb_27
115 116 2 gb_27
115 117 2 gb_27
118 119 2 gb_5
118 120 2 gb_10
120 121 2 gb_2
120 122 2 gb_21
122 123 2 gb_27
122 128 2 gb_27
123 124 2 gb_27
124 125 2 gb_27
125 126 2 gb_6
125 127 2 gb_6
128 129 2 gb_5
128 130 2 gb_10
130 131 2 gb_2
130 132 2 gb_21
132 133 2 gb_27
132 137 2 gb_27
133 134 2 gb_27
134 135 2 gb_6
134 136 2 gb_6
137 138 2 gb_5
137 139 2 gb_10
139 140 2 gb_2
139 141 2 gb_21
141 142 2 gb_27
141 146 2 gb_27
142 143 2 gb_27
143 144 2 gb_27
143 145 2 gb_27
146 147 2 gb_5
146 148 2 gb_10
148 149 2 gb_2
148 150 2 gb_21
150 151 2 gb_27
150 155 2 gb_27
151 152 2 gb_27
151 153 2 gb_27
152 154 2 gb_27
155 156 2 gb_5
155 157 2 gb_10
157 158 2 gb_2
157 159 2 gb_21
159 160 2 gb_27
159 172 2 gb_27
160 161 2 gb_27
161 162 2 gb_27
162 163 2 gb_21
163 164 2 gb_2
163 165 2 gb_11
165 166 2 gb_11
165 169 2 gb_11
166 167 2 gb_2
166 168 2 gb_2
169 170 2 gb_2
169 171 2 gb_2
172 173 2 gb_5
172 174 2 gb_10
174 175 2 gb_2
174 176 2 gb_21
176 177 2 gb_27
176 189 2 gb_27
177 178 2 gb_27
178 179 2 gb_16
178 181 2 gb_16
179 180 2 gb_3
179 183 2 gb_16
181 182 2 gb_3
181 185 2 gb_16
183 184 2 gb_3
183 187 2 gb_16
185 186 2 gb_3
185 187 2 gb_16
187 188 2 gb_3
189 190 2 gb_5
189 191 2 gb_10
191 192 2 gb_2
191 193 2 gb_21
193 194 2 gb_27
193 207 2 gb_27
194 195 2 gb_27
195 196 2 gb_16
195 198 2 gb_16
196 197 2 gb_3
196 200 2 gb_16
198 199 2 gb_3
198 202 2 gb_16
200 201 2 gb_3
200 204 2 gb_16
202 203 2 gb_3
202 204 2 gb_16
204 205 2 gb_13
205 206 2 gb_1
207 208 2 gb_5
207 209 2 gb_10
209 210 2 gb_2
209 211 2 gb_21
211 212 2 gb_27
211 216 2 gb_27
212 213 2 gb_27
213 214 2 gb_6
213 215 2 gb_6
216 217 2 gb_5
216 218 2 gb_10
218 219 2 gb_2
218 220 2 gb_21
220 221 2 gb_27
220 227 2 gb_27
221 222 2 gb_27
222 223 2 gb_5
222 224 2 gb_9
224 225 2 gb_2
224 226 2 gb_2
227 228 2 gb_5
227 229 2 gb_10
229 230 2 gb_2
229 231 2 gb_21
231 232 2 gb_27
231 236 2 gb_27
232 233 2 gb_27
233 234 2 gb_27
233 235 2 gb_27
236 237 2 gb_5
236 238 2 gb_10
238 239 2 gb_2
238 240 2 gb_21
240 241 2 gb_27
240 248 2 gb_27
241 242 2 gb_27
242 243 2 gb_27
243 244 2 gb_5
243 245 2 gb_9
245 246 2 gb_2
245 247 2 gb_2
248 249 2 gb_5
248 250 2 gb_10
250 251 2 gb_2
250 252 2 gb_21
252 253 2 gb_27
252 260 2 gb_27
253 254 2 gb_27
254 255 2 gb_27
255 256 2 gb_5
255 257 2 gb_9
257 258 2 gb_2
257 259 2 gb_2
260 261 2 gb_5
260 262 2 gb_10
262 263 2 gb_2
262 264 2 gb_21
264 265 2 gb_27
264 278 2 gb_27
265 266 2 gb_27
266 267 2 gb_16
266 269 2 gb_16
267 268 2 gb_3
267 271 2 gb_16
269 270 2 gb_3
269 273 2 gb_16
271 272 2 gb_3
271 275 2 gb_16
273 274 2 gb_3
273 275 2 gb_16
275 276 2 gb_13
276 277 2 gb_1
278 279 2 gb_5
278 280 2 gb_10
280 281 2 gb_2
280 282 2 gb_21
282 283 2 gb_27
282 287 2 gb_27
283 284 2 gb_27
284 285 2 gb_27
284 286 2 gb_27
287 288 2 gb_5
287 289 2 gb_10
289 290 2 gb_2
289 291 2 gb_21
291 292 2 gb_27
291 298 2 gb_27
292 293 2 gb_27
293 294 2 gb_5
293 295 2 gb_9
295 296 2 gb_2
295 297 2 gb_2
298 299 2 gb_5
298 300 2 gb_10
300 301 2 gb_2
300 302 2 gb_21
302 303 2 gb_27
302 306 2 gb_27
303 304 2 gb_27
303 305 2 gb_27
306 307 2 gb_5
306 308 2 gb_10
308 309 2 gb_2
308 310 2 gb_21
310 311 2 gb_27
310 314 2 gb_27
311 312 2 gb_27
311 313 2 gb_27
314 315 2 gb_5
314 316 2 gb_10
316 317 2 gb_2
316 318 2 gb_21
318 319 2 gb_27
318 323 2 gb_27
319 320 2 gb_18
319 322 2 gb_27
320 321 2 gb_1
323 324 2 gb_5
323 325 2 gb_10
325 326 2 gb_2
325 327 2 gb_21
327 328 2 gb_27
327 340 2 gb_27
328 329 2 gb_27
329 330 2 gb_27
330 331 2 gb_21
331 332 2 gb_2
331 333 2 gb_11
333 334 2 gb_11
333 337 2 gb_11
334 335 2 gb_2
334 336 2 gb_2
337 338 2 gb_2
337 339 2 gb_2
340 341 2 gb_5
340 342 2 gb_10
342 343 2 gb_2
342 344 2 gb_21
344 345 2 gb_27
344 354 2 gb_27
345 346 2 gb_27
346 347 2 gb_10
346 348 2 gb_10
347 350 2 gb_10
348 349 2 gb_3
348 352 2 gb_10
350 351 2 gb_3
350 352 2 gb_10
352 353 2 gb_2
354 355 2 gb_5
354 356 2 gb_10
356 357 2 gb_2
356 358 2 gb_21
358 359 2 gb_27
358 371 2 gb_27
359 360 2 gb_27
360 361 2 gb_27
361 362 2 gb_21
362 363 2 gb_2
362 364 2 gb_11
364 365 2 gb_11
364 368 2 gb_11
365 366 2 gb_2
365 367 2 gb_2
368 369 2 gb_2
368 370 2 gb_2
371 372 2 gb_5
371 373 2 gb_10
373 374 2 gb_2
373 375 2 gb_21
375 376 2 gb_27
375 389 2 gb_27
376 377 2 gb_27
377 378 2 gb_16
377 380 2 gb_16
378 379 2 gb_3
378 382 2 gb_16
380 381 2 gb_3
380 384 2 gb_16
382 383 2 gb_3
382 386 2 gb_16
384 385 2 gb_3
384 386 2 gb_16
386 387 2 gb_13
387 388 2 gb_1
389 390 2 gb_6
389 391 2 gb_6
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
2 6 1
3 6 1
4 6 1
5 9 1
5 12 1
6 10 1
6 11 1
6 13 1
7 9 1
7 12 1
8 14 1
8 15 1
9 16 1
9 17 1
10 14 1
10 15 1
11 13 1
12 13 1
13 18 1
13 21 1
14 16 1
14 17 1
15 19 1
15 22 1
15 23 1
16 18 1
16 21 1
17 20 1
17 24 1
17 25 1
18 22 1
18 23 1
19 21 1
21 26 1
21 33 1
22 24 1
22 25 1
23 27 1
23 34 1
23 35 1
24 26 1
24 33 1
25 28 1
25 36 1
25 39 1
26 29 1
26 30 1
26 34 1
26 35 1
27 31 1
27 32 1
27 33 1
29 31 1
29 32 1
33 37 1
33 38 1
33 40 1
34 36 1
34 39 1
35 41 1
35 42 1
36 43 1
36 44 1
37 41 1
37 42 1
38 40 1
39 40 1
40 45 1
40 49 1
41 43 1
41 44 1
42 46 1
42 48 1
42 50 1
42 51 1
43 45 1
43 49 1
44 47 1
44 52 1
44 53 1
45 50 1
45 51 1
46 49 1
47 48 1
48 49 1
49 54 1
49 67 1
50 52 1
50 53 1
51 55 1
51 68 1
51 69 1
52 54 1
52 67 1
53 56 1
53 58 1
53 70 1
53 73 1
54 68 1
54 69 1
55 67 1
60 66 1
62 66 1
67 71 1
67 72 1
67 74 1
68 70 1
68 73 1
69 75 1
69 76 1
70 77 1
70 78 1
71 75 1
71 76 1
72 74 1
73 74 1
74 79 1
75 77 1
75 78 1
76 80 1
76 81 1
77 79 1
78 82 1
78 83 1
79 84 1
79 88 1
80 82 1
80 83 1
81 85 1
81 89 1
81 90 1
82 84 1
82 88 1
83 86 1
83 87 1
83 91 1
83 92 1
84 89 1
84 90 1
85 88 1
88 93 1
88 97 1
89 91 1
89 92 1
90 94 1
90 98 1
90 99 1
91 93 1
91 97 1
92 95 1
92 96 1
92 100 1
92 101 1
93 98 1
93 99 1
94 97 1
97 102 1
97 103 1
98 100 1
98 101 1
99 104 1
99 105 1
100 102 1
100 103 1
101 106 1
101 109 1
102 104 1
102 105 1
103 107 1
103 108 1
103 110 1
104 106 1
104 109 1
105 111 1
105 112 1
106 113 1
106 114 1
107 111 1
107 112 1
108 110 1
109 110 1
110 115 1
110 118 1
111 113 1
111 114 1
112 116 1
112 117 1
112 119 1
112 120 1
113 115 1
113 118 1
114 121 1
114 122 1
115 119 1
115 120 1
116 118 1
117 118 1
118 123 1
118 128 1
119 121 1
119 122 1
120 124 1
120 129 1
120 130 1
121 123 1
121 128 1
122 125 1
122 131 1
122 132 1
123 126 1
123 127 1
123 129 1
123 130 1
124 128 1
128 133 1
128 137 1
129 131 1
129 132 1
130 134 1
130 138 1
130 139 1
131 133 1
131 137 1
132 135 1
132 136 1
132 140 1
132 141 1
133 138 1
133 139 1
134 137 1
137 142 1
137 146 1
138 140 1
138 141 1
139 143 1
139 147 1
139 148 1
140 142 1
140 146 1
141 144 1
141 145 1
141 149 1
141 150 1
142 147 1
142 148 1
143 146 1
146 151 1
146 155 1
147 149 1
147 150 1
148 152 1
148 153 1
148 156 1
148 157 1
149 151 1
149 155 1
150 154 1
150 158 1
150 159 1
151 156 1
151 157 1
152 155 1
153 154 1
153 155 1
155 160 1
155 172 1
156 158 1
156 159 1
157 161 1
157 173 1
157 174 1
158 160 1
158 172 1
159 162 1
159 175 1
159 176 1
160 163 1
160 173 1
160 174 1
161 164 1
161 165 1
161 172 1
162 166 1
162 169 1
163 167 1
163 168 1
163 170 1
163 171 1
164 166 1
164 169 1
166 170 1
166 171 1
167 169 1
168 169 1
172 177 1
172 189 1
173 175 1
173 176 1
174 178 1
174 190 1
174 191 1
175 177 1
175 189 1
176 179 1
176 181 1
176 192 1
176 193 1
177 190 1
177 191 1
178 189 1
189 194 1
189 207 1
190 192 1
190 193 1
191 195 1
191 208 1
191 209 1
192 194 1
192 207 1
193 196 1
193 198 1
193 210 1
193 211 1
194 208 1
194 209 1
195 207 1
200 206 1
202 206 1
207 212 1
207 216 1
208 210 1
208 211 1
209 213 1
209 217 1
209 218 1
210 212 1
210 216 1
211 214 1
211 215 1
211 219 1
211 220 1
212 217 1
212 218 1
213 216 1
216 221 1
216 227 1
217 219 1
217 220 1
218 222 1
218 228 1
218 229 1
219 221 1
219 227 1
220 223 1
220 224 1
220 230 1
220 231 1
221 225 1
221 226 1
221 228 1
221 229 1
222 227 1
223 225 1
223 226 1
227 232 1
227 236 1
228 230 1
228 231 1
229 233 1
229 237 1
229 238 1
230 232 1
230 236 1
231 234 1
231 235 1
231 239 1
231 240 1
232 237 1
232 238 1
233 236 1
236 241 1
236 248 1
237 239 1
237 240 1
238 242 1
238 249 1
238 250 1
239 241 1
239 248 1
240 243 1
240 251 1
240 252 1
241 244 1
241 245 1
241 249 1
241 250 1
242 246 1
242 247 1
242 248 1
244 246 1
244 247 1
248 253 1
248 260 1
249 251 1
249 252 1
250 254 1
250 261 1
250 262 1
251 253 1
251 260 1
252 255 1
252 263 1
252 264 1
253 256 1
253 257 1
253 261 1
253 262 1
254 258 1
254 259 1
254 260 1
256 258 1
256 259 1
260 265 1
260 278 1
261 263 1
261 264 1
262 266 1
262 279 1
262 280 1
263 265 1
263 278 1
264 267 1
264 269 1
264 281 1
264 282 1
265 279 1
265 280 1
266 278 1
271 277 1
273 277 1
278 283 1
278 287 1
279 281 1
279 282 1
280 284 1
280 288 1
280 289 1
281 283 1
281 287 1
282 285 1
282 286 1
282 290 1
282 291 1
283 288 1
283 289 1
284 287 1
287 292 1
287 298 1
288 290 1
288 291 1
289 293 1
289 299 1
289 300 1
290 292 1
290 298 1
291 294 1
291 295 1
291 301 1
291 302 1
292 296 1
292 297 1
292 299 1
292 300 1
293 298 1
294 296 1
294 297 1
298 303 1
298 306 1
299 301 1
299 302 1
300 304 1
300 305 1
300 307 1
300 308 1
301 303 1
301 306 1
302 309 1
302 310 1
303 307 1
303 308 1
304 306 1
305 306 1
306 311 1
306 314 1
307 309 1
307 310 1
308 312 1
308 313 1
308 315 1
308 316 1
309 311 1
309 314 1
310 317 1
310 318 1
311 315 1
311 316 1
312 314 1
313 314 1
314 319 1
314 323 1
315 317 1
315 318 1
316 320 1
316 322 1
316 324 1
316 325 1
317 319 1
317 323 1
318 321 1
318 326 1
318 327 1
319 324 1
319 325 1
320 323 1
321 322 1
322 323 1
323 328 1
323 340 1
324 326 1
324 327 1
325 329 1
325 341 1
325 342 1
326 328 1
326 340 1
327 330 1
327 343 1
327 344 1
328 331 1
328 341 1
328 342 1
329 332 1
329 333 1
329 340 1
330 334 1
330 337 1
331 335 1
331 336 1
331 338 1
331 339 1
332 334 1
332 337 1
334 338 1
334 339 1
335 337 1
336 337 1
340 345 1
340 354 1
341 343 1
341 344 1
342 346 1
342 355 1
342 356 1
343 345 1
343 354 1
344 347 1
344 348 1
344 357 1
344 358 1
345 355 1
345 356 1
346 354 1
354 359 1
354 371 1
355 357 1
355 358 1
356 360 1
356 372 1
356 373 1
357 359 1
357 371 1
358 361 1
358 374 1
358 375 1
359 362 1
359 372 1
359 373 1
360 363 1
360 364 1
360 371 1
361 365 1
361 368 1
362 366 1
362 367 1
362 369 1
362 370 1
363 365 1
363 368 1
365 369 1
365 370 1
366 368 1
367 368 1
371 376 1
371 389 1
372 374 1
372 375 1
373 377 1
373 390 1
373 391 1
374 376 1
374 389 1
375 378 1
375 380 1
376 390 1
376 391 1
377 389 1
382 388 1
384 388 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 2 ga_10
2 1 4 2 ga_10
2 1 5 2 ga_11
3 1 4 2 ga_10
3 1 5 2 ga_11
4 1 5 2 ga_11
1 5 6 2 ga_13
5 6 7 2 ga_30
5 6 8 2 ga_19
7 6 8 2 ga_33
6 8 9 2 ga_31
6 8 12 2 ga_31
9 8 12 2 ga_21
8 9 10 2 ga_13
8 9 13 2 ga_13
10 9 13 2 ga_13
9 10 11 2 ga_13
10 11 12 2 ga_13
8 12 11 2 ga_13
9 13 14 2 ga_30
9 13 15 2 ga_19
14 13 15 2 ga_33
13 15 16 2 ga_32
13 15 17 2 ga_31
16 15 17 2 ga_18
15 17 18 2 ga_13
15 17 21 2 ga_13
18 17 21 2 ga_13
17 18 19 2 ga_13
18 19 20 2 ga_12
17 21 22 2 ga_30
17 21 23 2 ga_19
22 21 23 2 ga_33
21 23 24 2 ga_32
21 23 25 2 ga_31
24 23 25 2 ga_18
23 25 26 2 ga_13
23 25 33 2 ga_13
26 25 33 2 ga_13
25 26 27 2 ga_15
26 27 28 2 ga_15
27 28 29 2 ga_30
27 28 30 2 ga_19
29 28 30 2 ga_33
28 30 31 2 ga_23
28 30 32 2 ga_23
31 30 32 2 ga_24
25 33 34 2 ga_30
25 33 35 2 ga_19
34 33 35 2 ga_33
33 35 36 2 ga_31
33 35 39 2 ga_31
36 35 39 2 ga_21
35 36 37 2 ga_13
35 36 40 2 ga_13
37 36 40 2 ga_13
36 37 38 2 ga_13
37 38 39 2 ga_13
35 39 38 2 ga_13
36 40 41 2 ga_30
36 40 42 2 ga_19
41 40 42 2 ga_33
40 42 43 2 ga_32
40 42 44 2 ga_31
43 42 44 2 ga_18
42 44 45 2 ga_13
42 44 49 2 ga_13
45 44 49 2 ga_13
44 45 46 2 ga_13
44 45 48 2 ga_15
46 45 48 2 ga_15
45 46 47 2 ga_12
44 49 50 2 ga_30
44 49 51 2 ga_19
50 49 51 2 ga_33
49 51 52 2 ga_32
49 51 53 2 ga_31
52 51 53 2 ga_18
51 53 54 2 ga_13
51 53 67 2 ga_13
54 53 67 2 ga_13
53 54 55 2 ga_15
54 55 56 2 ga_27
54 55 58 2 ga_27
56 55 58 2 ga_27
55 56 57 2 ga_25
55 56 60 2 ga_27
57 56 60 2 ga_25
55 58 59 2 ga_25
55 58 62 2 ga_27
59 58 62 2 ga_25
56 60 61 2 ga_25
56 60 64 2 ga_27
61 60 64 2 ga_25
58 62 63 2 ga_25
58 62 64 2 ga_27
63 62 64 2 ga_25
60 64 62 2 ga_27
60 64 65 2 ga_27
62 64 65 2 ga_27
64 65 66 2 ga_12
53 67 68 2 ga_30
53 67 69 2 ga_19
68 67 69 2 ga_33
67 69 70 2 ga_31
67 69 73 2 ga_31
70 69 73 2 ga_21
69 70 71 2 ga_13
69 70 74 2 ga_13
71 70 74 2 ga_13
70 71 72 2 ga_13
71 72 73 2 ga_13
69 73 72 2 ga_13
70 74 75 2 ga_30
70 74 76 2 ga_19
75 74 76 2 ga_33
74 76 77 2 ga_32
74 76 78 2 ga_31
77 76 78 2 ga_18
76 78 79 2 ga_13
78 79 80 2 ga_30
78 79 81 2 ga_19
80 79 81 2 ga_33
79 81 82 2 ga_32
79 81 83 2 ga_31
82 81 83 2 ga_18
81 83 84 2 ga_13
81 83 88 2 ga_13
84 83 88 2 ga_13
83 84 85 2 ga_15
84 85 86 2 ga_22
84 85 87 2 ga_22
86 85 87 2 ga_38
83 88 89 2 ga_30
83 88 90 2 ga_19
89 88 90 2 ga_33
88 90 91 2 ga_32
88 90 92 2 ga_31
91 90 92 2 ga_18
90 92 93 2 ga_13
90 92 97 2 ga_13
93 92 97 2 ga_13
92 93 94 2 ga_15
93 94 95 2 ga_22
93 94 96 2 ga_22
95 94 96 2 ga_38
92 97 98 2 ga_30
92 97 99 2 ga_19
98 97 99 2 ga_33
97 99 100 2 ga_32
97 99 101 2 ga_31
100 99 101 2 ga_18
99 101 102 2 ga_13
99 101 103 2 ga_13
102 101 103 2 ga_13
101 103 104 2 ga_30
101 103 105 2 ga_19
104 103 105 2 ga_33
103 105 106 2 ga_31
103 105 109 2 ga_31
106 105 109 2 ga_21
105 106 107 2 ga_13
105 106 110 2 ga_13
107 106 110 2 ga_13
106 107 108 2 ga_13
107 108 109 2 ga_13
105 109 108 2 ga_13
106 110 111 2 ga_30
106 110 112 2 ga_19
111 110 112 2 ga_33
110 112 113 2 ga_32
110 112 114 2 ga_31
113 112 114 2 ga_18
112 114 115 2 ga_13
112 114 118 2 ga_13
115 114 118 2 ga_13
114 115 116 2 ga_15
114 115 117 2 ga_15
116 115 117 2 ga_15
114 118 119 2 ga_30
114 118 120 2 ga_19
119 118 120 2 ga_33
118 120 121 2 ga_32
118 120 122 2 ga_31
121 120 122 2 ga_18
120 122 123 2 ga_13
120 122 128 2 ga_13
123 122 128 2 ga_13
122 123 124 2 ga_15
123 124 125 2 ga_15
124 125 126 2 ga_22
124 125 127 2 ga_22
126 125 127 2 ga_38
122 128 129 2 ga_30
122 128 130 2 ga_19
129 128 130 2 ga_33
128 130 131 2 ga_32
128 130 132 2 ga_31
131 130 132 2 ga_18
130 132 133 2 ga_13
130 132 137 2 ga_13
133 132 137 2 ga_13
132 133 134 2 ga_15
133 134 135 2 ga_22
133 134 136 2 ga_22
135 134 136 2 ga_38
132 137 138 2 ga_30
132 137 139 2 ga_19
138 137 139 2 ga_33
137 139 140 2 ga_32
137 139 141 2 ga_31
140 139 141 2 ga_18
139 141 142 2 ga_13
139 141 146 2 ga_13
142 141 146 2 ga_13
141 142 143 2 ga_15
142 143 144 2 ga_15
142 143 145 2 ga_15
144 143 145 2 ga_15
141 146 147 2 ga_30
141 146 148 2 ga_19
147 146 148 2 ga_33
146 148 149 2 ga_32
146 148 150 2 ga_31
149 148 150 2 ga_18
148 150 151 2 ga_13
148 150 155 2 ga_13
151 150 155 2 ga_13
150 151 152 2 ga_15
150 151 153 2 ga_15
152 151 153 2 ga_15
151 152 154 2 ga_15
150 155 156 2 ga_30
150 155 157 2 ga_19
156 155 157 2 ga_33
155 157 158 2 ga_32
155 157 159 2 ga_31
158 157 159 2 ga_18
157 159 160 2 ga_13
157 159 172 2 ga_13
160 159 172 2 ga_13
159 160 161 2 ga_15
160 161 162 2 ga_15
161 162 163 2 ga_13
162 163 164 2 ga_20
162 163 165 2 ga_33
164 163 165 2 ga_23
163 165 166 2 ga_28
163 165 169 2 ga_28
166 165 169 2 ga_28
165 166 167 2 ga_23
165 166 168 2 ga_23
167 166 168 2 ga_24
165 169 170 2 ga_23
165 169 171 2 ga_23
170 169 171 2 ga_24
159 172 173 2 ga_30
159 172 174 2 ga_19
173 172 174 2 ga_33
172 174 175 2 ga_32
172 174 176 2 ga_31
175 174 176 2 ga_18
174 176 177 2 ga_13
174 176 189 2 ga_13
177 176 189 2 ga_13
176 177 178 2 ga_15
177 178 179 2 ga_27
177 178 181 2 ga_27
179 178 181 2 ga_27
178 179 180 2 ga_25
178 179 183 2 ga_27
180 179 183 2 ga_25
178 181 182 2 ga_25
178 181 185 2 ga_27
182 181 185 2 ga_25
179 183 184 2 ga_25
179 183 187 2 ga_27
184 183 187 2 ga_25
181 185 186 2 ga_25
181 185 187 2 ga_27
186 185 187 2 ga_25
183 187 185 2 ga_27
183 187 188 2 ga_25
185 187 188 2 ga_25
176 189 190 2 ga_30
176 189 191 2 ga_19
190 189 191 2 ga_33
189 191 192 2 ga_32
189 191 193 2 ga_31
192 191 193 2 ga_18
191 193 194 2 ga_13
191 193 207 2 ga_13
194 193 207 2 ga_13
193 194 195 2 ga_15
194 195 196 2 ga_27
194 195 198 2 ga_27
196 195 198 2 ga_27
195 196 197 2 ga_25
195 196 200 2 ga_27
197 196 200 2 ga_25
195 198 199 2 ga_25
195 198 202 2 ga_27
199 198 202 2 ga_25
196 200 201 2 ga_25
196 200 204 2 ga_27
201 200 204 2 ga_25
198 202 203 2 ga_25
198 202 204 2 ga_27
203 202 204 2 ga_25
200 204 202 2 ga_27
200 204 205 2 ga_27
202 204 205 2 ga_27
204 205 206 2 ga_12
193 207 208 2 ga_30
193 207 209 2 ga_19
208 207 209 2 ga_33
207 209 210 2 ga_32
207 209 211 2 ga_31
210 209 211 2 ga_18
209 211 212 2 ga_13
209 211 216 2 ga_13
212 211 216 2 ga_13
211 212 213 2 ga_15
212 213 214 2 ga_22
212 213 215 2 ga_22
214 213 215 2 ga_38
211 216 217 2 ga_30
211 216 218 2 ga_19
217 216 218 2 ga_33
216 218 219 2 ga_32
216 218 220 2 ga_31
219 218 220 2 ga_18
218 220 221 2 ga_13
218 220 227 2 ga_13
221 220 227 2 ga_13
220 221 222 2 ga_15
221 222 223 2 ga_30
221 222 224 2 ga_19
223 222 224 2 ga_33
222 224 225 2 ga_23
222 224 226 2 ga_23
225 224 226 2 ga_24
220 227 228 2 ga_30
220 227 229 2 ga_19
228 227 229 2 ga_33
227 229 230 2 ga_32
227 229 231 2 ga_31
230 229 231 2 ga_18
229 231 232 2 ga_13
229 231 236 2 ga_13
232 231 236 2 ga_13
231 232 233 2 ga_15
232 233 234 2 ga_15
232 233 235 2 ga_15
234 233 235 2 ga_15
231 236 237 2 ga_30
231 236 238 2 ga_19
237 236 238 2 ga_33
236 238 239 2 ga_32
236 238 240 2 ga_31
239 238 240 2 ga_18
238 240 241 2 ga_13
238 240 248 2 ga_13
241 240 248 2 ga_13
240 241 242 2 ga_15
241 242 243 2 ga_15
242 243 244 2 ga_30
242 243 245 2 ga_19
244 243 245 2 ga_33
243 245 246 2 ga_23
243 245 247 2 ga_23
246 245 247 2 ga_24
240 248 249 2 ga_30
240 248 250 2 ga_19
249 248 250 2 ga_33
248 250 251 2 ga_32
248 250 252 2 ga_31
251 250 252 2 ga_18
250 252 253 2 ga_13
250 252 260 2 ga_13
253 252 260 2 ga_13
252 253 254 2 ga_15
253 254 255 2 ga_15
254 255 256 2 ga_30
254 255 257 2 ga_19
256 255 257 2 ga_33
255 257 258 2 ga_23
255 257 259 2 ga_23
258 257 259 2 ga_24
252 260 261 2 ga_30
252 260 262 2 ga_19
261 260 262 2 ga_33
260 262 263 2 ga_32
260 262 264 2 ga_31
263 262 264 2 ga_18
262 264 265 2 ga_13
262 264 278 2 ga_13
265 264 278 2 ga_13
264 265 266 2 ga_15
265 266 267 2 ga_27
265 266 269 2 ga_27
267 266 269 2 ga_27
266 267 268 2 ga_25
266 267 271 2 ga_27
268 267 271 2 ga_25
266 269 270 2 ga_25
266 269 273 2 ga_27
270 269 273 2 ga_25
267 271 272 2 ga_25
267 271 275 2 ga_27
272 271 275 2 ga_25
269 273 274 2 ga_25
269 273 275 2 ga_27
274 273 275 2 ga_25
271 275 273 2 ga_27
271 275 276 2 ga_27
273 275 276 2 ga_27
275 276 277 2 ga_12
264 278 279 2 ga_30
264 278 280 2 ga_19
279 278 280 2 ga_33
278 280 281 2 ga_32
278 280 282 2 ga_31
281 280 282 2 ga_18
280 282 283 2 ga_13
280 282 287 2 ga_13
283 282 287 2 ga_13
282 283 284 2 ga_15
283 284 285 2 ga_15
283 284 286 2 ga_15
285 284 286 2 ga_15
282 287 288 2 ga_30
282 287 289 2 ga_19
288 287 289 2 ga_33
287 289 290 2 ga_32
287 289 291 2 ga_31
290 289 291 2 ga_18
289 291 292 2 ga_13
289 291 298 2 ga_13
292 291 298 2 ga_13
291 292 293 2 ga_15
292 293 294 2 ga_30
292 293 295 2 ga_19
294 293 295 2 ga_33
293 295 296 2 ga_23
293 295 297 2 ga_23
296 295 297 2 ga_24
291 298 299 2 ga_30
291 298 300 2 ga_19
299 298 300 2 ga_33
298 300 301 2 ga_32
298 300 302 2 ga_31
301 300 302 2 ga_18
300 302 303 2 ga_13
300 302 306 2 ga_13
303 302 306 2 ga_13
302 303 304 2 ga_15
302 303 305 2 ga_15
304 303 305 2 ga_15
302 306 307 2 ga_30
302 306 308 2 ga_19
307 306 308 2 ga_33
306 308 309 2 ga_32
306 308 310 2 ga_31
309 308 310 2 ga_18
308 310 311 2 ga_13
308 310 314 2 ga_13
311 310 314 2 ga_13
310 311 312 2 ga_15
310 311 313 2 ga_15
312 311 313 2 ga_15
310 314 315 2 ga_30
310 314 316 2 ga_19
315 314 316 2 ga_33
314 316 317 2 ga_32
314 316 318 2 ga_31
317 316 318 2 ga_18
316 318 319 2 ga_13
316 318 323 2 ga_13
319 318 323 2 ga_13
318 319 320 2 ga_13
318 319 322 2 ga_15
320 319 322 2 ga_15
319 320 321 2 ga_12
318 323 324 2 ga_30
318 323 325 2 ga_19
324 323 325 2 ga_33
323 325 326 2 ga_32
323 325 327 2 ga_31
326 325 327 2 ga_18
325 327 328 2 ga_13
325 327 340 2 ga_13
328 327 340 2 ga_13
327 328 329 2 ga_15
328 329 330 2 ga_15
329 330 331 2 ga_13
330 331 332 2 ga_20
330 331 333 2 ga_33
332 331 333 2 ga_23
331 333 334 2 ga_28
331 333 337 2 ga_28
334 333 337 2 ga_28
333 334 335 2 ga_23
333 334 336 2 ga_23
335 334 336 2 ga_24
333 337 338 2 ga_23
333 337 339 2 ga_23
338 337 339 2 ga_24
327 340 341 2 ga_30
327 340 342 2 ga_19
341 340 342 2 ga_33
340 342 343 2 ga_32
340 342 344 2 ga_31
343 342 344 2 ga_18
342 344 345 2 ga_13
342 344 354 2 ga_13
345 344 354 2 ga_13
344 345 346 2 ga_15
345 346 347 2 ga_37
345 346 348 2 ga_37
347 346 348 2 ga_7
346 347 350 2 ga_7
346 348 349 2 ga_36
346 348 352 2 ga_7
349 348 352 2 ga_36
347 350 351 2 ga_36
347 350 352 2 ga_7
351 350 352 2 ga_36
348 352 350 2 ga_7
348 352 353 2 ga_36
350 352 353 2 ga_36
344 354 355 2 ga_30
344 354 356 2 ga_19
355 354 356 2 ga_33
354 356 357 2 ga_32
354 356 358 2 ga_31
357 356 358 2 ga_18
356 358 359 2 ga_13
356 358 371 2 ga_13
359 358 371 2 ga_13
358 359 360 2 ga_15
359 360 361 2 ga_15
360 361 362 2 ga_13
361 362 363 2 ga_20
361 362 364 2 ga_33
363 362 364 2 ga_23
362 364 365 2 ga_28
362 364 368 2 ga_28
365 364 368 2 ga_28
364 365 366 2 ga_23
364 365 367 2 ga_23
366 365 367 2 ga_24
364 368 369 2 ga_23
364 368 370 2 ga_23
369 368 370 2 ga_24
358 371 372 2 ga_30
358 371 373 2 ga_19
372 371 373 2 ga_33
371 373 374 2 ga_32
371 373 375 2 ga_31
374 373 375 2 ga_18
373 375 376 2 ga_13
373 375 389 2 ga_13
376 375 389 2 ga_13
375 376 377 2 ga_15
376 377 378 2 ga_27
376 377 380 2 ga_27
378 377 380 2 ga_27
377 378 379 2 ga_25
377 378 382 2 ga_27
379 378 382 2 ga_25
377 380 381 2 ga_25
377 380 384 2 ga_27
381 380 384 2 ga_25
378 382 383 2 ga_25
378 382 386 2 ga_27
383 382 386 2 ga_25
380 384 385 2 ga_25
380 384 386 2 ga_27
385 384 386 2 ga_25
382 386 384 2 ga_27
382 386 387 2 ga_27
384 386 387 2 ga_27
386 387 388 2 ga_12
375 389 390 2 ga_22
375 389 391 2 ga_22
390 389 391 2 ga_38
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 1 gd_39
1 5 6 8 1 gd_42
1 5 6 8 1 gd_45
5 6 8 9 1 gd_14
6 8 9 13 1 gd_43
6 8 9 13 1 gd_44
9 8 12 11 1 gd_39
8 9 10 11 1 gd_34
8 9 13 15 1 gd_42
8 9 13 15 1 gd_45
9 10 11 12 1 gd_34
10 11 12 8 1 gd_34
9 13 15 17 1 gd_14
13 15 17 21 1 gd_43
13 15 17 21 1 gd_44
15 17 18 19 1 gd_34
15 17 21 23 1 gd_42
15 17 21 23 1 gd_45
17 18 19 20 1 gd_23
17 21 23 25 1 gd_14
21 23 25 33 1 gd_43
21 23 25 33 1 gd_44
23 25 26 27 1 gd_34
23 25 33 35 1 gd_42
23 25 33 35 1 gd_45
25 26 27 28 1 gd_34
26 27 28 30 1 gd_40
27 28 30 31 1 gd_14
25 33 35 36 1 gd_14
33 35 36 40 1 gd_43
33 35 36 40 1 gd_44
36 35 39 38 1 gd_39
35 36 37 38 1 gd_34
35 36 40 42 1 gd_42
35 36 40 42 1 gd_45
36 37 38 39 1 gd_34
37 38 39 35 1 gd_34
36 40 42 44 1 gd_14
40 42 44 49 1 gd_43
40 42 44 49 1 gd_44
42 44 45 46 1 gd_34
42 44 49 51 1 gd_42
42 44 49 51 1 gd_45
44 45 46 47 1 gd_23
44 49 51 53 1 gd_14
49 51 53 67 1 gd_43
49 51 53 67 1 gd_44
51 53 54 55 1 gd_34
51 53 67 69 1 gd_42
51 53 67 69 1 gd_45
53 54 55 56 1 gd_40
60 64 65 66 1 gd_11
53 67 69 70 1 gd_14
67 69 70 74 1 gd_43
67 69 70 74 1 gd_44
70 69 73 72 1 gd_39
69 70 71 72 1 gd_34
69 70 74 76 1 gd_42
69 70 74 76 1 gd_45
70 71 72 73 1 gd_34
71 72 73 69 1 gd_34
70 74 76 78 1 gd_14
74 76 78 79 1 gd_43
74 76 78 79 1 gd_44
76 78 79 81 1 gd_42
76 78 79 81 1 gd_45
78 79 81 83 1 gd_14
79 81 83 88 1 gd_43
79 81 83 88 1 gd_44
81 83 84 85 1 gd_34
81 83 88 90 1 gd_42
81 83 88 90 1 gd_45
83 84 85 86 1 gd_40
83 88 90 92 1 gd_14
88 90 92 97 1 gd_43
88 90 92 97 1 gd_44
90 92 93 94 1 gd_34
90 92 97 99 1 gd_42
90 92 97 99 1 gd_45
92 93 94 95 1 gd_40
92 97 99 101 1 gd_14
97 99 101 103 1 gd_43
97 99 101 103 1 gd_44
99 101 103 105 1 gd_42
99 101 103 105 1 gd_45
101 103 105 106 1 gd_14
103 105 106 110 1 gd_43
103 105 106 110 1 gd_44
106 105 109 108 1 gd_39
105 106 107 108 1 gd_34
105 106 110 112 1 gd_42
105 106 110 112 1 gd_45
106 107 108 109 1 gd_34
107 108 109 105 1 gd_34
106 110 112 114 1 gd_14
110 112 114 118 1 gd_43
110 112 114 118 1 gd_44
112 114 115 116 1 gd_34
112 114 118 120 1 gd_42
112 114 118 120 1 gd_45
114 118 120 122 1 gd_14
118 120 122 128 1 gd_43
118 120 122 128 1 gd_44
120 122 123 124 1 gd_34
120 122 128 130 1 gd_42
120 122 128 130 1 gd_45
122 123 124 125 1 gd_34
123 124 125 127 1 gd_40
122 128 130 132 1 gd_14
128 130 132 137 1 gd_43
128 130 132 137 1 gd_44
130 132 133 134 1 gd_34
130 132 137 139 1 gd_42
130 132 137 139 1 gd_45
132 133 134 135 1 gd_40
132 137 139 141 1 gd_14
137 139 141 146 1 gd_43
137 139 141 146 1 gd_44
139 141 142 143 1 gd_34
139 141 146 148 1 gd_42
139 141 146 148 1 gd_45
141 142 143 144 1 gd_34
141 146 148 150 1 gd_14
146 148 150 155 1 gd_43
146 148 150 155 1 gd_44
148 150 151 152 1 gd_34
148 150 155 157 1 gd_42
148 150 155 157 1 gd_45
150 151 152 154 1 gd_34
150 155 157 159 1 gd_14
155 157 159 172 1 gd_43
155 157 159 172 1 gd_44
157 159 160 161 1 gd_34
157 159 172 174 1 gd_42
157 159 172 174 1 gd_45
159 160 161 162 1 gd_34
160 161 162 163 1 gd_34
161 162 163 165 1 gd_39
162 163 165 166 1 gd_14
163 165 166 167 1 gd_14
163 165 169 170 1 gd_14
159 172 174 176 1 gd_14
172 174 176 189 1 gd_43
172 174 176 189 1 gd_44
174 176 177 178 1 gd_34
174 176 189 191 1 gd_42
174 176 189 191 1 gd_45
176 177 178 179 1 gd_40
176 189 191 193 1 gd_14
189 191 193 207 1 gd_43
189 191 193 207 1 gd_44
191 193 194 195 1 gd_34
191 193 207 209 1 gd_42
191 193 207 209 1 gd_45
193 194 195 196 1 gd_40
200 204 205 206 1 gd_11
193 207 209 211 1 gd_14
207 209 211 216 1 gd_43
207 209 211 216 1 gd_44
209 211 212 213 1 gd_34
209 211 216 218 1 gd_42
209 211 216 218 1 gd_45
211 212 213 214 1 gd_40
211 216 218 220 1 gd_14
216 218 220 227 1 gd_43
216 218 220 227 1 gd_44
218 220 221 222 1 gd_34
218 220 227 229 1 gd_42
218 220 227 229 1 gd_45
220 221 222 224 1 gd_40
221 222 224 225 1 gd_14
220 227 229 231 1 gd_14
227 229 231 236 1 gd_43
227 229 231 236 1 gd_44
229 231 232 233 1 gd_34
229 231 236 238 1 gd_42
229 231 236 238 1 gd_45
231 232 233 234 1 gd_34
231 236 238 240 1 gd_14
236 238 240 248 1 gd_43
236 238 240 248 1 gd_44
238 240 241 242 1 gd_34
238 240 248 250 1 gd_42
238 240 248 250 1 gd_45
240 241 242 243 1 gd_34
241 242 243 245 1 gd_40
242 243 245 246 1 gd_14
240 248 250 252 1 gd_14
248 250 252 260 1 gd_43
248 250 252 260 1 gd_44
250 252 253 254 1 gd_34
250 252 260 262 1 gd_42
250 252 260 262 1 gd_45
252 253 254 255 1 gd_34
253 254 255 257 1 gd_40
254 255 257 258 1 gd_14
252 260 262 264 1 gd_14
260 262 264 278 1 gd_43
260 262 264 278 1 gd_44
262 264 265 266 1 gd_34
262 264 278 280 1 gd_42
262 264 278 280 1 gd_45
264 265 266 267 1 gd_40
271 275 276 277 1 gd_11
264 278 280 282 1 gd_14
278 280 282 287 1 gd_43
278 280 282 287 1 gd_44
280 282 283 284 1 gd_34
280 282 287 289 1 gd_42
280 282 287 289 1 gd_45
282 283 284 285 1 gd_34
282 287 289 291 1 gd_14
287 289 291 298 1 gd_43
287 289 291 298 1 gd_44
289 291 292 293 1 gd_34
289 291 298 300 1 gd_42
289 291 298 300 1 gd_45
291 292 293 295 1 gd_40
292 293 295 296 1 gd_14
291 298 300 302 1 gd_14
298 300 302 306 1 gd_43
298 300 302 306 1 gd_44
300 302 303 304 1 gd_34
300 302 306 308 1 gd_42
300 302 306 308 1 gd_45
302 306 308 310 1 gd_14
306 308 310 314 1 gd_43
306 308 310 314 1 gd_44
308 310 311 312 1 gd_34
308 310 314 316 1 gd_42
308 310 314 316 1 gd_45
310 314 316 318 1 gd_14
314 316 318 323 1 gd_43
314 316 318 323 1 gd_44
316 318 319 320 1 gd_34
316 318 323 325 1 gd_42
316 318 323 325 1 gd_45
318 319 320 321 1 gd_23
318 323 325 327 1 gd_14
323 325 327 340 1 gd_43
323 325 327 340 1 gd_44
325 327 328 329 1 gd_34
325 327 340 342 1 gd_42
325 327 340 342 1 gd_45
327 328 329 330 1 gd_34
328 329 330 331 1 gd_34
329 330 331 333 1 gd_39
330 331 333 334 1 gd_14
331 333 334 335 1 gd_14
331 333 337 338 1 gd_14
327 340 342 344 1 gd_14
340 342 344 354 1 gd_43
340 342 344 354 1 gd_44
342 344 345 346 1 gd_34
342 344 354 356 1 gd_42
342 344 354 356 1 gd_45
344 345 346 347 1 gd_40
344 354 356 358 1 gd_14
354 356 358 371 1 gd_43
354 356 358 371 1 gd_44
356 358 359 360 1 gd_34
356 358 371 373 1 gd_42
356 358 371 373 1 gd_45
358 359 360 361 1 gd_34
359 360 361 362 1 gd_34
360 361 362 364 1 gd_39
361 362 364 365 1 gd_14
362 364 365 366 1 gd_14
362 364 368 369 1 gd_14
358 371 373 375 1 gd_14
371 373 375 389 1 gd_43
371 373 375 389 1 gd_44
373 375 376 377 1 gd_34
373 375 389 391 1 gd_42
373 375 389 391 1 gd_45
375 376 377 378 1 gd_40
382 386 387 388 1 gd_11
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
6 5 8 7 2 gi_1
8 6 9 12 2 gi_1
9 8 13 10 2 gi_2
13 9 15 14 2 gi_1
15 13 17 16 2 gi_1
17 15 21 18 2 gi_2
21 17 23 22 2 gi_1
23 21 25 24 2 gi_1
25 23 33 26 2 gi_2
27 30 29 28 2 gi_1
28 32 31 30 2 gi_1
33 25 35 34 2 gi_1
35 33 36 39 2 gi_1
36 35 40 37 2 gi_2
40 36 42 41 2 gi_1
42 40 44 43 2 gi_1
44 42 49 45 2 gi_2
44 48 46 45 2 gi_2
49 44 51 50 2 gi_1
51 49 53 52 2 gi_1
53 51 67 54 2 gi_2
54 58 56 55 2 gi_1
55 56 60 64 2 gi_1
55 58 62 64 2 gi_1
56 55 60 57 2 gi_1
56 55 58 62 2 gi_1
56 60 64 62 2 gi_1
58 55 62 59 2 gi_1
58 55 56 60 2 gi_1
58 62 64 60 2 gi_1
60 64 56 61 2 gi_1
62 64 58 63 2 gi_1
64 60 62 65 2 gi_1
67 53 69 68 2 gi_1
69 67 70 73 2 gi_1
70 69 74 71 2 gi_2
74 70 76 75 2 gi_1
76 74 78 77 2 gi_1
79 78 81 80 2 gi_1
81 79 83 82 2 gi_1
83 81 88 84 2 gi_2
84 87 86 85 2 gi_1
88 83 90 89 2 gi_1
90 88 92 91 2 gi_1
92 90 97 93 2 gi_2
93 96 95 94 2 gi_1
97 92 99 98 2 gi_1
99 97 101 100 2 gi_1
101 99 103 102 2 gi_2
103 101 105 104 2 gi_1
105 103 106 109 2 gi_1
106 105 110 107 2 gi_2
110 106 112 111 2 gi_1
112 110 114 113 2 gi_1
114 112 118 115 2 gi_2
114 116 117 115 2 gi_2
118 114 120 119 2 gi_1
120 118 122 121 2 gi_1
122 120 128 123 2 gi_2
124 127 126 125 2 gi_1
128 122 130 129 2 gi_1
130 128 132 131 2 gi_1
132 130 137 133 2 gi_2
133 136 135 134 2 gi_1
137 132 139 138 2 gi_1
139 137 141 140 2 gi_1
141 139 146 142 2 gi_2
142 144 145 143 2 gi_2
146 141 148 147 2 gi_1
148 146 150 149 2 gi_1
150 148 155 151 2 gi_2
150 153 152 151 2 gi_2
155 150 157 156 2 gi_1
157 155 159 158 2 gi_1
159 157 172 160 2 gi_2
163 162 165 164 2 gi_1
163 169 166 165 2 gi_1
165 168 167 166 2 gi_1
165 171 170 169 2 gi_1
172 159 174 173 2 gi_1
174 172 176 175 2 gi_1
176 174 189 177 2 gi_2
177 181 179 178 2 gi_1
178 179 183 187 2 gi_1
178 181 185 187 2 gi_1
179 178 183 180 2 gi_1
179 178 181 185 2 gi_1
179 183 187 185 2 gi_1
181 178 185 182 2 gi_1
181 178 179 183 2 gi_1
181 185 187 183 2 gi_1
183 187 179 184 2 gi_1
185 187 181 186 2 gi_1
187 183 185 188 2 gi_1
189 176 191 190 2 gi_1
191 189 193 192 2 gi_1
193 191 207 194 2 gi_2
194 198 196 195 2 gi_1
195 196 200 204 2 gi_1
195 198 202 204 2 gi_1
196 195 200 197 2 gi_1
196 195 198 202 2 gi_1
196 200 204 202 2 gi_1
198 195 202 199 2 gi_1
198 195 196 200 2 gi_1
198 202 204 200 2 gi_1
200 204 196 201 2 gi_1
202 204 198 203 2 gi_1
204 200 202 205 2 gi_1
207 193 209 208 2 gi_1
209 207 211 210 2 gi_1
211 209 216 212 2 gi_2
212 215 214 213 2 gi_1
216 211 218 217 2 gi_1
218 216 220 219 2 gi_1
220 218 227 221 2 gi_2
221 224 223 222 2 gi_1
222 226 225 224 2 gi_1
227 220 229 228 2 gi_1
229 227 231 230 2 gi_1
231 229 236 232 2 gi_2
232 234 235 233 2 gi_2
236 231 238 237 2 gi_1
238 236 240 239 2 gi_1
240 238 248 241 2 gi_2
242 245 244 243 2 gi_1
243 247 246 245 2 gi_1
248 240 250 249 2 gi_1
250 248 252 251 2 gi_1
252 250 260 253 2 gi_2
254 257 256 255 2 gi_1
255 259 258 257 2 gi_1
260 252 262 261 2 gi_1
262 260 264 263 2 gi_1
264 262 278 265 2 gi_2
265 269 267 266 2 gi_1
266 267 271 275 2 gi_1
266 269 273 275 2 gi_1
267 266 271 268 2 gi_1
267 266 269 273 2 gi_1
267 271 275 273 2 gi_1
269 266 273 270 2 gi_1
269 266 267 271 2 gi_1
269 273 275 271 2 gi_1
271 275 267 272 2 gi_1
273 275 269 274 2 gi_1
275 271 273 276 2 gi_1
278 264 280 279 2 gi_1
280 278 282 281 2 gi_1
282 280 287 283 2 gi_2
283 285 286 284 2 gi_2
287 282 289 288 2 gi_1
289 287 291 290 2 gi_1
291 289 298 292 2 gi_2
292 295 294 293 2 gi_1
293 297 296 295 2 gi_1
298 291 300 299 2 gi_1
300 298 302 301 2 gi_1
302 300 306 303 2 gi_2
302 304 305 303 2 gi_2
306 302 308 307 2 gi_1
308 306 310 309 2 gi_1
310 308 314 311 2 gi_2
310 312 313 311 2 gi_2
314 310 316 315 2 gi_1
316 314 318 317 2 gi_1
318 316 323 319 2 gi_2
318 322 320 319 2 gi_2
323 318 325 324 2 gi_1
325 323 327 326 2 gi_1
327 325 340 328 2 gi_2
331 330 333 332 2 gi_1
331 337 334 333 2 gi_1
333 336 335 334 2 gi_1
333 339 338 337 2 gi_1
340 327 342 341 2 gi_1
342 340 344 343 2 gi_1
344 342 354 345 2 gi_2
345 348 347 346 2 gi_1
346 348 352 350 2 gi_1
346 347 350 352 2 gi_1
347 350 352 348 2 gi_1
347 346 348 352 2 gi_1
348 346 352 349 2 gi_1
348 346 347 350 2 gi_1
350 347 352 351 2 gi_1
352 348 350 353 2 gi_1
354 344 356 355 2 gi_1
356 354 358 357 2 gi_1
358 356 371 359 2 gi_2
362 361 364 363 2 gi_1
362 368 365 364 2 gi_1
364 367 366 365 2 gi_1
364 370 369 368 2 gi_1
371 358 373 372 2 gi_1
373 371 375 374 2 gi_1
375 373 389 376 2 gi_2
376 380 378 377 2 gi_1
377 378 382 386 2 gi_1
377 380 384 386 2 gi_1
378 377 382 379 2 gi_1
378 377 380 384 2 gi_1
378 382 386 384 2 gi_1
380 377 384 381 2 gi_1
380 377 378 382 2 gi_1
380 384 386 382 2 gi_1
382 386 378 383 2 gi_1
384 386 380 385 2 gi_1
386 382 384 387 2 gi_1
389 375 391 390 2 gi_1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "gromos54a7.ff/spce.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 "gromos54a7.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
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