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Commit 8e995a20 authored by Peter Eastman's avatar Peter Eastman
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GromacsTopFile supports all terms needed for CHARMM force field

parent 84165803
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Showing with 108 additions and 30 deletions
wrappers/python/simtk/openmm/app/gromacstopfile.py
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...@@ -59,21 +59,24 @@ class GromacsTopFile(object): ...@@ -59,21 +59,24 @@ class GromacsTopFile(object):
self.dihedrals = [] self.dihedrals = []
self.exclusions = [] self.exclusions = []
self.pairs = [] self.pairs = []
self.cmaps = []
def _processFile(self, file): def _processFile(self, file):
append = '' append = ''
for line in open(file): for line in open(file):
if line.strip().endswith('\\'): if line.strip().endswith('\\'):
append += line[:line.rfind('\\')] append = '%s %s' % (append, line[:line.rfind('\\')])
else: else:
self._processLine(append+line, file) self._processLine(append+' '+line, file)
append = '' append = ''
def _processLine(self, line, file): def _processLine(self, line, file):
"""Process one line from a file.""" """Process one line from a file."""
if ';' in line:
line = line[:line.index(';')]
stripped = line.strip() stripped = line.strip()
ignore = not all(self._ifStack) ignore = not all(self._ifStack)
if line.startswith('*') or stripped.startswith(';') or len(stripped) == 0: if stripped.startswith('*') or len(stripped) == 0:
# A comment or empty line. # A comment or empty line.
return return
...@@ -147,6 +150,8 @@ class GromacsTopFile(object): ...@@ -147,6 +150,8 @@ class GromacsTopFile(object):
self._processExclusion(line) self._processExclusion(line)
elif self._currentCategory == 'pairs': elif self._currentCategory == 'pairs':
self._processPair(line) self._processPair(line)
elif self._currentCategory == 'cmap':
self._processCmap(line)
elif self._currentCategory == 'atomtypes': elif self._currentCategory == 'atomtypes':
self._processAtomType(line) self._processAtomType(line)
elif self._currentCategory == 'bondtypes': elif self._currentCategory == 'bondtypes':
...@@ -159,6 +164,8 @@ class GromacsTopFile(object): ...@@ -159,6 +164,8 @@ class GromacsTopFile(object):
self._processImplicitType(line) self._processImplicitType(line)
elif self._currentCategory == 'pairtypes': elif self._currentCategory == 'pairtypes':
self._processPairType(line) self._processPairType(line)
elif self._currentCategory == 'cmaptypes':
self._processCmapType(line)
def _processDefaults(self, line): def _processDefaults(self, line):
"""Process the [ defaults ] line.""" """Process the [ defaults ] line."""
...@@ -216,7 +223,7 @@ class GromacsTopFile(object): ...@@ -216,7 +223,7 @@ 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] != '1': if fields[3] not in ('1', '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)
...@@ -227,7 +234,7 @@ class GromacsTopFile(object): ...@@ -227,7 +234,7 @@ class GromacsTopFile(object):
fields = line.split() fields = line.split()
if len(fields) < 5: if len(fields) < 5:
raise ValueError('Too few fields in [ dihedrals ] line: '+line); raise ValueError('Too few fields in [ dihedrals ] line: '+line);
if fields[4] not in ('1', '3', '4', '9'): if fields[4] not in ('1', '2', '3', '4', '9'):
raise ValueError('Unsupported function type in [ dihedrals ] line: '+line); raise ValueError('Unsupported function type in [ dihedrals ] line: '+line);
self._currentMoleculeType.dihedrals.append(fields) self._currentMoleculeType.dihedrals.append(fields)
...@@ -251,6 +258,15 @@ class GromacsTopFile(object): ...@@ -251,6 +258,15 @@ class GromacsTopFile(object):
raise ValueError('Unsupported function type in [ pairs ] line: '+line); raise ValueError('Unsupported function type in [ pairs ] line: '+line);
self._currentMoleculeType.pairs.append(fields) self._currentMoleculeType.pairs.append(fields)
def _processCmap(self, line):
"""Process a line in the [ cmaps ] category."""
if self._currentMoleculeType is None:
raise ValueError('Found [ cmap ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 6:
raise ValueError('Too few fields in [ pairs ] line: '+line);
self._currentMoleculeType.cmaps.append(fields)
def _processAtomType(self, line): def _processAtomType(self, line):
"""Process a line in the [ atomtypes ] category.""" """Process a line in the [ atomtypes ] category."""
fields = line.split() fields = line.split()
...@@ -272,7 +288,7 @@ class GromacsTopFile(object): ...@@ -272,7 +288,7 @@ class GromacsTopFile(object):
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] != '1': if fields[3] not in ('1', '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
...@@ -281,7 +297,7 @@ class GromacsTopFile(object): ...@@ -281,7 +297,7 @@ class GromacsTopFile(object):
fields = line.split() fields = line.split()
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', '3', '4', '9'): if fields[4] not in ('1', '2', '3', '4', '9'):
raise ValueError('Unsupported function type in [ dihedraltypes ] line: '+line); raise ValueError('Unsupported function type in [ dihedraltypes ] line: '+line);
key = tuple(fields[:5]) key = tuple(fields[:5])
if fields[4] == '9' and key in self._dihedralTypes: if fields[4] == '9' and key in self._dihedralTypes:
...@@ -304,8 +320,17 @@ class GromacsTopFile(object): ...@@ -304,8 +320,17 @@ class GromacsTopFile(object):
raise ValueError('Too few fields in [ pairtypes] line: '+line); raise ValueError('Too few fields in [ pairtypes] line: '+line);
if fields[2] != '1': if fields[2] != '1':
raise ValueError('Unsupported function type in [ pairtypes ] line: '+line); raise ValueError('Unsupported function type in [ pairtypes ] line: '+line);
self._pairTypes[fields[0]] = fields self._pairTypes[tuple(fields[:2])] = fields
def _processCmapType(self, line):
"""Process a line in the [ cmaptypes ] category."""
fields = line.split()
if len(fields) < 8 or len(fields) < 8+int(fields[6])*int(fields[7]):
raise ValueError('Too few fields in [ cmaptypes ] line: '+line);
if fields[5] != '1':
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line);
self._cmapTypes[tuple(fields[:5])] = fields
def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}): def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}):
"""Load a top file. """Load a top file.
...@@ -332,6 +357,7 @@ class GromacsTopFile(object): ...@@ -332,6 +357,7 @@ class GromacsTopFile(object):
self._dihedralTypes = {} self._dihedralTypes = {}
self._implicitTypes = {} self._implicitTypes = {}
self._pairTypes = {} self._pairTypes = {}
self._cmapTypes = {}
self._processFile(file) self._processFile(file)
# Create the Topology from it. # Create the Topology from it.
...@@ -426,6 +452,9 @@ class GromacsTopFile(object): ...@@ -426,6 +452,9 @@ class GromacsTopFile(object):
angles = None angles = None
periodic = None periodic = None
rb = None rb = None
harmonicTorsion = None
cmap = None
mapIndices = {}
bondIndices = [] bondIndices = []
topologyAtoms = list(self.topology.atoms()) topologyAtoms = list(self.topology.atoms())
exceptions = [] exceptions = []
...@@ -499,11 +528,11 @@ class GromacsTopFile(object): ...@@ -499,11 +528,11 @@ class GromacsTopFile(object):
atoms = [int(x)-1 for x in fields[:3]] atoms = [int(x)-1 for x in fields[:3]]
types = tuple(atomTypes[i] for i in atoms) types = tuple(atomTypes[i] for i in atoms)
if len(fields) >= 6: if len(fields) >= 6:
params = fields[4:6] params = fields[4:]
elif types in self._angleTypes: elif types in self._angleTypes:
params = self._angleTypes[types][4:6] params = self._angleTypes[types][4:]
elif types[::-1] in self._angleTypes: elif types[::-1] in self._angleTypes:
params = self._angleTypes[types[::-1]][4:6] params = self._angleTypes[types[::-1]][4:]
else: else:
raise ValueError('No parameters specified for angle: '+fields[0]+', '+fields[1]+', '+fields[2]) raise ValueError('No parameters specified for angle: '+fields[0]+', '+fields[1]+', '+fields[2])
# Decide whether to use a constraint or a bond. # Decide whether to use a constraint or a bond.
...@@ -530,7 +559,15 @@ class GromacsTopFile(object): ...@@ -530,7 +559,15 @@ class GromacsTopFile(object):
angles = mm.HarmonicAngleForce() angles = mm.HarmonicAngleForce()
sys.addForce(angles) sys.addForce(angles)
angles.addAngle(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], theta, float(params[1])) angles.addAngle(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], theta, float(params[1]))
if fields[3] == '5':
# This is a Urey-Bradley term, so add the bond.
if bonds is None:
bonds = mm.HarmonicBondForce()
sys.addForce(bonds)
k = float(params[3])
if k != 0:
bonds.addBond(baseAtomIndex+atoms[0], baseAtomIndex+atoms[2], float(params[2]), k)
# Add torsions. # Add torsions.
for fields in moleculeType.dihedrals: for fields in moleculeType.dihedrals:
...@@ -539,8 +576,8 @@ class GromacsTopFile(object): ...@@ -539,8 +576,8 @@ class GromacsTopFile(object):
dihedralType = fields[4] dihedralType = fields[4]
reversedTypes = types[::-1]+(dihedralType,) reversedTypes = types[::-1]+(dihedralType,)
types = types+(dihedralType,) types = types+(dihedralType,)
if (dihedralType == '1' and len(fields) > 7) or (dihedralType == '3' and len(fields) > 10): if (dihedralType in ('1', '2') and len(fields) > 7) or (dihedralType == '3' and len(fields) > 10):
params = fields paramsList = [fields]
else: else:
# Look for a matching dihedral type. # Look for a matching dihedral type.
paramsList = None paramsList = None
...@@ -551,22 +588,63 @@ class GromacsTopFile(object): ...@@ -551,22 +588,63 @@ class GromacsTopFile(object):
break break
if paramsList is None: if paramsList is None:
raise ValueError('No parameters specified for dihedral: '+fields[0]+', '+fields[1]+', '+fields[2]+', '+fields[3]) raise ValueError('No parameters specified for dihedral: '+fields[0]+', '+fields[1]+', '+fields[2]+', '+fields[3])
for params in paramsList: for params in paramsList:
if dihedralType in ('1', '4', '9'): if dihedralType in ('1', '4', '9'):
k = float(params[6]) # Periodic torsion
if k != 0: k = float(params[6])
if periodic is None: if k != 0:
periodic = mm.PeriodicTorsionForce() if periodic is None:
sys.addForce(periodic) periodic = mm.PeriodicTorsionForce()
periodic.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], int(params[7]), float(params[5])*degToRad, k) sys.addForce(periodic)
else: periodic.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], int(params[7]), float(params[5])*degToRad, k)
c = [float(x) for x in params[5:11]] elif dihedralType == '2':
if any(x != 0 for x in c): # Harmonic torsion
if rb is None: k = float(params[6])
rb = mm.RBTorsionForce() if k != 0:
sys.addForce(rb) if harmonicTorsion is None:
rb.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], c[0], c[1], c[2], c[3], c[4], c[5]) harmonicTorsion = mm.CustomTorsionForce('0.5*k*(theta-theta0)^2')
harmonicTorsion.addPerTorsionParameter('theta0')
harmonicTorsion.addPerTorsionParameter('k')
sys.addForce(harmonicTorsion)
harmonicTorsion.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], (float(params[5])*degToRad, k))
else:
# RB Torsion
c = [float(x) for x in params[5:11]]
if any(x != 0 for x in c):
if rb is None:
rb = mm.RBTorsionForce()
sys.addForce(rb)
rb.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], c[0], c[1], c[2], c[3], c[4], c[5])
# Add CMAP terms.
for fields in moleculeType.cmaps:
atoms = [int(x)-1 for x in fields[:5]]
types = tuple(atomTypes[i] for i in atoms)
if len(fields) >= 8 and len(fields) >= 8+int(fields[6])*int(fields[7]):
params = fields
elif types in self._cmapTypes:
params = self._cmapTypes[types]
elif types[::-1] in self._cmapTypes:
params = self._cmapTypes[types[::-1]]
else:
raise ValueError('No parameters specified for cmap: '+fields[0]+', '+fields[1]+', '+fields[2]+', '+fields[3]+', '+fields[4])
if cmap is None:
cmap = mm.CMAPTorsionForce()
sys.addForce(cmap)
mapSize = int(params[6])
if mapSize != int(params[7]):
raise ValueError('Non-square CMAPs are not supported')
map = []
for i in range(mapSize):
for j in range(mapSize):
map.append(float(params[8+mapSize*((j+mapSize/2)%mapSize)+((i+mapSize/2)%mapSize)]))
map = tuple(map)
if map not in mapIndices:
mapIndices[map] = cmap.addMap(mapSize, map)
cmap.addTorsion(mapIndices[map], baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3],
baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], baseAtomIndex+atoms[4])
# Set nonbonded parameters for particles. # Set nonbonded parameters for particles.
for fields in moleculeType.atoms: for fields in moleculeType.atoms:
......
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