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Unverified Commit 69aa6760 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2008 from sunhwan/master 

handles virtual_sites2 and nbfix in gromacs topology
parents 8bddf3fe 6b4d27e9
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Showing with 435 additions and 13 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 69aa6760
......@@ -342,9 +342,9 @@ class CharmmPsfFile(object):
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
if numlp != 0 or numlph != 0:
raise NotImplemented('Cannot currently handle PSFs with lone '
'pairs defined in the NUMLP/NUMLPH '
'section.')
raise NotImplementedError('Cannot currently handle PSFs with lone '
'pairs defined in the NUMLP/NUMLPH '
'section.')
# Now do the CMAPs
ncrterm = conv(psfsections['NCRTERM'][0], int, 'Number of cross-terms')
holder = psfsections['NCRTERM'][1]
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 69aa6760
......@@ -43,7 +43,8 @@ import math
import os
import re
import distutils.spawn
from collections import OrderedDict
from collections import OrderedDict, defaultdict
from itertools import combinations, combinations_with_replacement
HBonds = ff.HBonds
AllBonds = ff.AllBonds
......@@ -115,7 +116,9 @@ class GromacsTopFile(object):
self.exclusions = []
self.pairs = []
self.cmaps = []
self.vsites2 = []
self.has_virtual_sites = False
self.has_nbfix_terms = False
def _processFile(self, file):
append = ''
......@@ -249,6 +252,10 @@ class GromacsTopFile(object):
self._processPairType(line)
elif self._currentCategory == 'cmaptypes':
self._processCmapType(line)
elif self._currentCategory == 'nonbond_params':
self._processNonbondType(line)
elif self._currentCategory == 'virtual_sites2':
self._processVirtualSites2(line)
elif self._currentCategory.startswith('virtual_sites'):
if self._currentMoleculeType is None:
raise ValueError('Found %s before [ moleculetype ]' %
......@@ -435,6 +442,22 @@ class GromacsTopFile(object):
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line)
self._cmapTypes[tuple(fields[:5])] = fields
def _processNonbondType(self, line):
"""Process a line in the [ nonbond_params ] category."""
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ nonbond_params ] line: '+line)
if fields[2] != '1':
raise ValueError('Unsupported function type in [ nonbond_params ] line: '+line)
self._nonbondTypes[tuple(sorted(fields[:2]))] = fields
def _processVirtualSites2(self, line):
"""Process a line in the [ virtual_sites2 ] category."""
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ virtual_sites2 ] line: ' + line)
self._currentMoleculeType.vsites2.append(fields[:5])
def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
"""Load a top file.
......@@ -484,6 +507,7 @@ class GromacsTopFile(object):
self._implicitTypes = {}
self._pairTypes = {}
self._cmapTypes = {}
self._nonbondTypes = {}
self._processFile(file)
# Create the Topology from it.
......@@ -643,6 +667,24 @@ class GromacsTopFile(object):
for types in dihedralTypeTable.values():
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:
# Build a lookup table and angle/dihedral indices list to
# let us handle exclusion manually.
angleIndices = []
torsionIndices = []
atom_partners = defaultdict(lambda : defaultdict(set))
atom_charges = []
# Loop over molecules and create the specified number of each type.
for moleculeName, moleculeCount in self._molecules:
......@@ -840,18 +882,25 @@ class GromacsTopFile(object):
for fields in moleculeType.atoms:
params = self._atomTypes[fields[1]]
if len(fields) > 6:
q = float(fields[6])
else:
q = float(params[4])
if self._defaults[1] == '1':
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)
lj.addParticle([float(params[6]), float(params[7])])
elif self._defaults[1] == '2':
nb.addParticle(q, float(params[6]), float(params[7]))
atom_charges.append(q)
else:
if self._defaults[1] == '1':
nb.addParticle(q, 1.0, 0.0)
lj.addParticle([float(params[6]), float(params[7])])
elif self._defaults[1] == '2':
nb.addParticle(q, float(params[6]), float(params[7]))
for fields in moleculeType.atoms:
if implicitSolvent is OBC2:
if fields[1] not in self._implicitTypes:
raise ValueError('No implicit solvent parameters specified for atom type: '+fields[1])
......@@ -860,6 +909,23 @@ class GromacsTopFile(object):
for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]]
bondIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1]))
if has_nbfix_terms:
for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]]
atom_partners[baseAtomIndex+atoms[0]]['bond'].add(baseAtomIndex+atoms[1])
atom_partners[baseAtomIndex+atoms[1]]['bond'].add(baseAtomIndex+atoms[0])
for fields in moleculeType.angles:
atoms = [int(x)-1 for x in fields[:3]]
angleIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2]))
for pair in combinations(atoms, 2):
atom_partners[baseAtomIndex+pair[0]]['angle'].add(baseAtomIndex+pair[1])
atom_partners[baseAtomIndex+pair[1]]['angle'].add(baseAtomIndex+pair[0])
for fields in moleculeType.dihedrals:
atoms = [int(x)-1 for x in fields[:4]]
torsionIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3]))
for pair in combinations(atoms, 2):
atom_partners[baseAtomIndex+pair[0]]['torsion'].add(baseAtomIndex+pair[1])
atom_partners[baseAtomIndex+pair[1]]['torsion'].add(baseAtomIndex+pair[0])
# Record nonbonded exceptions.
......@@ -886,16 +952,70 @@ class GromacsTopFile(object):
if atom > atoms[0]:
exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom))
# Record virtual sites
for fields in moleculeType.vsites2:
atoms = [int(x)-1 for x in fields[:3]]
c1 = float(fields[4])
vsite = mm.TwoParticleAverageSite(baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], (1-c1), c1)
sys.setVirtualSite(baseAtomIndex+atoms[0], vsite)
# Create nonbonded exceptions.
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, fudgeLJ)
if not has_nbfix_terms:
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, fudgeLJ)
else:
excluded_atom_pairs = set() # save these pairs so we don't zero them out
for tor in torsionIndices:
# First check to see if atoms 1 and 4 are already excluded because
# they are 1-2 or 1-3 pairs (would happen in 6-member rings or
# fewer). Then check that they're not already added as exclusions
if 'bond' in atom_partners[tor[3]] and tor[0] in atom_partners[tor[3]]['bond']: continue
if 'angle' in atom_partners[tor[3]] and tor[0] in atom_partners[tor[3]]['angle']: continue
key = min((tor[0], tor[3]),
(tor[3], tor[0]))
if key in excluded_atom_pairs: continue # multiterm...
params1 = self._atomTypes[atom_types[tor[0]]]
params4 = self._atomTypes[atom_types[tor[3]]]
q1 = atom_charges[tor[0]]
rmin1 = float(params1[6])
eps1 = float(params1[7])
q4 = atom_charges[tor[3]]
rmin4 = float(params4[6])
eps4 = float(params4[7])
charge_prod = (q1*q4)
epsilon = (math.sqrt(abs(eps1 * eps4)))
rmin14 = (rmin1 + rmin4) / 2
nb.addException(tor[0], tor[3], charge_prod, rmin14, epsilon)
excluded_atom_pairs.add(key)
# Add excluded atoms
for atom_idx, atom in atom_partners.items():
# Exclude all bonds and angles
for atom2 in atom['bond']:
if atom2 > atom_idx:
nb.addException(atom_idx, atom2, 0.0, 1.0, 0.0)
excluded_atom_pairs.add((atom_idx, atom2))
for atom2 in atom['angle']:
if ((atom_idx, atom2) in excluded_atom_pairs):
continue
if atom2 > atom_idx:
nb.addException(atom_idx, atom2, 0.0, 1.0, 0.0)
excluded_atom_pairs.add((atom_idx, atom2))
for atom2 in atom['dihedral']:
if atom2 <= atom_idx: continue
if ((atom_idx, atom2) in excluded_atom_pairs):
continue
nb.addException(atom_idx, atom2, 0.0, 1.0, 0.0)
for exclusion in exclusions:
nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True)
if self._defaults[1] == '1':
# We're using a CustomNonbondedForce for LJ interactions, so also create a CustomBondForce
# to handle the exceptions.
pair_bond = mm.CustomBondForce('138.935456*q/r-C/r^6+A/r^12')
pair_bond.addPerBondParameter('q')
pair_bond.addPerBondParameter('C')
......@@ -932,6 +1052,88 @@ class GromacsTopFile(object):
lj.setNonbondedMethod(methodMap[nonbondedMethod])
lj.setCutoffDistance(nonbondedCutoff)
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([])
for pair in self._nonbondTypes:
atom_nbfix_types.add(pair[0])
atom_nbfix_types.add(pair[1])
lj_idx_list = [0 for _ in atom_types]
lj_radii, lj_depths = [], []
num_lj_types = 0
lj_type_list = []
for i,atom_type in enumerate(atom_types):
atom = self._atomTypes[atom_type]
if lj_idx_list[i]: continue # already assigned
atom_rmin = atom[6]
atom_epsilon = atom[7]
num_lj_types += 1
lj_idx_list[i] = num_lj_types
ljtype = (atom_rmin, atom_epsilon)
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)):
atom_type2 = atom_types[j]
if lj_idx_list[j] > 0: continue # already assigned
atom2 = self._atomTypes[atom_type2]
atom2_rmin = atom2[6]
atom2_epsilon = atom2[7]
if atom2 is atom:
lj_idx_list[j] = num_lj_types
elif atom_type not in atom_nbfix_types:
# Only non-NBFIXed atom types can be compressed
ljtype2 = (atom2_rmin, atom2_epsilon)
if ljtype == ljtype2:
lj_idx_list[j] = num_lj_types
# Now everything is assigned. Create the A-coefficient and
# B-coefficient arrays
acoef = [0 for i in range(num_lj_types*num_lj_types)]
bcoef = acoef[:]
for i in range(num_lj_types):
namei = lj_type_list[i][0]
for j in range(num_lj_types):
namej = lj_type_list[j][0]
try:
params = self._nonbondTypes[tuple(sorted((namei, namej)))]
rij = float(params[3])
wdij = float(params[4])
except KeyError:
rij = (lj_radii[i] + lj_radii[j]) / 2
wdij = math.sqrt(lj_depths[i] * lj_depths[j])
acoef[i+num_lj_types*j] = 2 * math.sqrt(wdij) * rij**6
bcoef[i+num_lj_types*j] = 4 * wdij * rij**6
cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6;'
'a=acoef(type1, type2);'
'b=bcoef(type1, type2)')
cforce.addTabulatedFunction('acoef',
mm.Discrete2DFunction(num_lj_types, num_lj_types, acoef))
cforce.addTabulatedFunction('bcoef',
mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef))
cforce.addPerParticleParameter('type')
if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)):
cforce.setNonbondedMethod(cforce.CutoffPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
cforce.setUseLongRangeCorrection(True)
elif nonbondedMethod is ff.NoCutoff:
cforce.setNonbondedMethod(cforce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic:
cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
else:
raise ValueError('Unrecognized nonbonded method')
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.
if hydrogenMass is not None:
......
wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py
View file @ 69aa6760
......@@ -531,7 +531,7 @@ class ResidueList(list):
return atom
def append(self, thing):
raise NotImplemented('Use "add_atom" to build a residue list')
raise NotImplementedError('Use "add_atom" to build a residue list')
extend = append
......
wrappers/python/tests/TestGromacsTopFile.py
View file @ 69aa6760
......@@ -151,6 +151,24 @@ class TestGromacsTopFile(unittest.TestCase):
totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
self.assertAlmostEqual(totalMass1, totalMass2)
def test_VirtualParticle(self):
"""Test virtual particle works correctly."""
top = GromacsTopFile('systems/bnz.top')
gro = GromacsGroFile('systems/bnz.gro')
system = top.createSystem()
self.assertEqual(26, system.getNumParticles())
self.assertEqual(1, len(top._moleculeTypes['BENX'].vsites2))
context = Context(system, VerletIntegrator(1*femtosecond),
Platform.getPlatformByName('Reference'))
context.setPositions(gro.positions)
context.computeVirtualSites()
ene = context.getState(getEnergy=True).getPotentialEnergy()
# the energy output is from gromacs and it only prints out 6 sig digits.
self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 1.88855e+02, places=3)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/bnz.gro 0 → 100644
View file @ 69aa6760
Gnomes, ROck Monsters And Chili Sauce
26
1BEN CG 1 0.052 -0.016 0.455
1BEN HG 2 0.064 -0.020 0.563
1BEN CD1 3 0.004 -0.129 0.386
1BEN HD1 4 -0.020 -0.219 0.441
1BEN CD2 5 0.084 0.100 0.385
1BEN HD2 6 0.120 0.187 0.438
1BEN CE1 7 -0.012 -0.125 0.247
1BEN HE1 8 -0.048 -0.211 0.194
1BEN CE2 9 0.069 0.104 0.245
1BEN HE2 10 0.094 0.194 0.191
1BEN CZ 11 0.022 -0.008 0.177
1BEN HZ 12 0.011 -0.005 0.069
1BEN LPA 13 0.037 -0.012 0.316
1BEN CG 14 0.036 0.038 -0.433
1BEN HG 15 0.092 0.057 -0.523
1BEN CD1 16 -0.054 -0.070 -0.428
1BEN HD1 17 -0.068 -0.133 -0.515
1BEN CD2 18 0.052 0.120 -0.321
1BEN HD2 19 0.120 0.205 -0.326
1BEN CE1 20 -0.127 -0.095 -0.311
1BEN HE1 21 -0.196 -0.178 -0.307
1BEN CE2 22 -0.019 0.094 -0.203
1BEN HE2 23 -0.004 0.157 -0.116
1BEN CZ 24 -0.108 -0.014 -0.198
1BEN HZ 25 -0.163 -0.034 -0.108
1BEN LPA 26 -0.036 0.012 -0.316
0.00000 0.00000 0.00000
wrappers/python/tests/systems/bnz.top 0 → 100644
View file @ 69aa6760
;
; File '6lyz_gmx.top' was generated
; By user: sunhwan (40816)
; On host: kuta
; At date: Fri Nov 10 13:02:26 2017
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2017-dev-20170822-762c6f0 (-:
;
; Executable: /home/sunhwan/local/gromacs/src/gromacs/build/bin/gmx
; Data prefix: /home/sunhwan/local/gromacs/src/gromacs (source tree)
; Working dir: /data/sunhwan/work/lysozyme/1_setup
; Command line:
; gmx pdb2gmx -f 6lyz_4pdb2gmx.pdb -o 6lyz_gmx.pdb -p 6lyz_gmx.top -ff charmm36 -water tip3p -ter -merge all
; Force field was read from current directory or a relative path - path added.
;
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
[ atomtypes ]
;type atnum mass charge ? sigma epsilon
CG2R61 6 12.011000 0.000 A 0.355005321205 0.29288
HGR61 1 1.008000 0.000 A 0.242003727796 0.12552
LP 0 0.000000 0.00 A 0.0 0.0 ; pram
; NBFIX for LP, rmin=1.2/2^(1/6), eps=4.184*.01
[ nonbond_params ]
LP LP 1 1.069078461768 0.041840000000 ; pram
[ bondtypes ]
; i j func b0 kb
CG2R61 CG2R61 1 0.13750000 255224.00
CG2R61 HGR61 1 0.10800000 284512.00
[ angletypes ]
; i j k func theta0 ktheta ub0 kub
CG2R61 CG2R61 CG2R61 5 120.000000 334.720000 0.24162000 29288.00
CG2R61 CG2R61 HGR61 5 120.000000 251.040000 0.21525000 18409.60
[ dihedraltypes ]
; i j k l func phi0 kphi mult
CG2R61 CG2R61 CG2R61 CG2R61 9 180.000000 12.970400 2
CG2R61 CG2R61 CG2R61 HGR61 9 180.000000 17.572800 2
HGR61 CG2R61 CG2R61 HGR61 9 180.000000 10.041600 2
[ dihedraltypes ]
; 'improper' dihedrals
; i j k l func phi0 kphi
[ moleculetype ]
; Name nrexcl
BENX 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 BENX rtp BENX q 0.0
1 CG2R61 1 BENX CG 1 -0.115 12.011 ; qtot -0.115
2 HGR61 1 BENX HG 1 0.115 1.008 ; qtot 0
3 CG2R61 1 BENX CD1 1 -0.115 12.011 ; qtot -0.115
4 HGR61 1 BENX HD1 1 0.115 1.008 ; qtot 0
5 CG2R61 1 BENX CD2 1 -0.115 12.011 ; qtot -0.115
6 HGR61 1 BENX HD2 1 0.115 1.008 ; qtot 0
7 CG2R61 1 BENX CE1 1 -0.115 12.011 ; qtot -0.115
8 HGR61 1 BENX HE1 1 0.115 1.008 ; qtot 0
9 CG2R61 1 BENX CE2 1 -0.115 12.011 ; qtot -0.115
10 HGR61 1 BENX HE2 1 0.115 1.008 ; qtot 0
11 CG2R61 1 BENX CZ 1 -0.115 12.011 ; qtot -0.115
12 HGR61 1 BENX HZ 1 0.115 1.008 ; qtot 0
13 LP 1 BENX LPA 1 0.000 0.000 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 5 1
3 4 1
3 7 1
5 6 1
5 9 1
7 8 1
7 11 1
9 10 1
9 11 1
11 12 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 10 1
1 11 1
2 4 1
2 6 1
2 7 1
2 9 1
3 6 1
3 9 1
3 12 1
4 5 1
4 8 1
4 11 1
5 7 1
5 12 1
6 10 1
6 11 1
7 10 1
8 9 1
8 12 1
10 12 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 5
2 1 5 5
3 1 5 5
1 3 4 5
1 3 7 5
4 3 7 5
1 5 6 5
1 5 9 5
6 5 9 5
3 7 8 5
3 7 11 5
8 7 11 5
5 9 10 5
5 9 11 5
10 9 11 5
7 11 9 5
7 11 12 5
9 11 12 5
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 3 4 9
2 1 3 7 9
5 1 3 4 9
5 1 3 7 9
2 1 5 6 9
2 1 5 9 9
3 1 5 6 9
3 1 5 9 9
1 3 7 8 9
1 3 7 11 9
4 3 7 8 9
4 3 7 11 9
1 5 9 10 9
1 5 9 11 9
6 5 9 10 9
6 5 9 11 9
3 7 11 9 9
3 7 11 12 9
8 7 11 9 9
8 7 11 12 9
5 9 11 7 9
5 9 11 12 9
10 9 11 7 9
10 9 11 12 9
[ virtual_sites2 ]
; Vsite from funct a
13 1 11 1 0.500
[ system ]
; Name
two benzene
[ molecules ]
; Compound #mols
BENX 2
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