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Commit c5ad2202 authored by peastman's avatar peastman
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ForceField supports DrudeForce

parent 6185317a
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Showing with 167 additions and 38 deletions
wrappers/python/simtk/openmm/app/forcefield.py
View file @ c5ad2202
......@@ -158,18 +158,20 @@ class ForceField(object):
if typeAttrib in attrib:
raise ValueError('Tag specifies both a type and a class for the same atom: '+etree.tostring(node))
if attrib[classAttrib] not in self._atomClasses:
return None # Unknown atom class
types.append(None) # Unknown atom class
else:
types.append(self._atomClasses[attrib[classAttrib]])
else:
if typeAttrib not in attrib or attrib[typeAttrib] not in self._atomTypes:
return None # Unknown atom type
types.append(None) # Unknown atom type
else:
types.append([attrib[typeAttrib]])
return types
def _parseTorsion(self, node):
"""Parse the node defining a torsion."""
types = self._findAtomTypes(node, 4)
if types is None:
if None in types:
return None
torsion = PeriodicTorsion(types)
attrib = node.attrib
......@@ -416,6 +418,12 @@ class ForceField(object):
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
# Let generators do postprocessing
for force in self._forces:
if 'postprocessSystem' in dir(force):
force.postprocessSystem(sys, data, args)
# Execute scripts found in the XML files.
for script in self._scripts:
......@@ -483,9 +491,10 @@ def _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch
if position == len(atoms):
return True
elem = atoms[position].element
name = atoms[position].name
for i in range(len(atoms)):
atom = template.atoms[i]
if (atom.element == elem or atom.element is None) and not hasMatch[i] and len(atom.bondedTo) == len(bondedTo[position]) and atom.externalBonds == externalBonds[position]:
if (atom.element == elem or (atom.element is None and atom.name == name)) and not hasMatch[i] and len(atom.bondedTo) == len(bondedTo[position]) and atom.externalBonds == externalBonds[position]:
# See if the bonds for this identification are consistent
allBondsMatch = all((bonded > position or matches[bonded] in atom.bondedTo for bonded in bondedTo[position]))
......@@ -521,7 +530,7 @@ class HarmonicBondGenerator:
ff._forces.append(generator)
for bond in element.findall('Bond'):
types = ff._findAtomTypes(bond, 2)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.length.append(float(bond.attrib['length']))
......@@ -569,7 +578,7 @@ class HarmonicAngleGenerator:
ff._forces.append(generator)
for angle in element.findall('Angle'):
types = ff._findAtomTypes(angle, 3)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.types3.append(types[2])
......@@ -748,11 +757,11 @@ class RBTorsionGenerator:
ff._forces.append(generator)
for torsion in element.findall('Proper'):
types = ff._findAtomTypes(torsion, 4)
if types is not None:
if None not in types:
generator.proper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
for torsion in element.findall('Improper'):
types = ff._findAtomTypes(torsion, 4)
if types is not None:
if None not in types:
generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
......@@ -850,7 +859,7 @@ class CMAPTorsionGenerator:
generator.maps.append(values)
for torsion in element.findall('Torsion'):
types = ff._findAtomTypes(torsion, 5)
if types is not None:
if None not in types:
generator.torsions.append(CMAPTorsion(types, int(torsion.attrib['map'])))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
......@@ -931,7 +940,7 @@ class NonbondedGenerator:
raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['sigma']), float(atom.attrib['epsilon']))
for t in types[0]:
generator.typeMap[t] = values
......@@ -952,7 +961,14 @@ class NonbondedGenerator:
force.addParticle(values[0], values[1], values[2])
else:
raise ValueError('No nonbonded parameters defined for atom type '+t)
# Create exceptions based on bonds and virtual sites.
force.setNonbondedMethod(methodMap[nonbondedMethod])
force.setCutoffDistance(nonbondedCutoff)
if 'ewaldErrorTolerance' in args:
force.setEwaldErrorTolerance(args['ewaldErrorTolerance'])
sys.addForce(force)
def postprocessSystem(self, sys, data, args):
# Create exceptions based on bonds, virtual sites, and Drude particles.
bondIndices = []
for bond in data.bonds:
bondIndices.append((bond.atom1, bond.atom2))
......@@ -961,12 +977,26 @@ class NonbondedGenerator:
site = sys.getVirtualSite(i)
for j in range(site.getNumParticles()):
bondIndices.append((i, site.getParticle(j)))
force.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale)
force.setNonbondedMethod(methodMap[nonbondedMethod])
force.setCutoffDistance(nonbondedCutoff)
if 'ewaldErrorTolerance' in args:
force.setEwaldErrorTolerance(args['ewaldErrorTolerance'])
sys.addForce(force)
drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)]
if len(drude) > 0:
drude = drude[0]
# For purposes of creating exceptions, a Drude particle is "bonded" to anything
# its parent atom is bonded to.
drudeMap = {}
for i in range(drude.getNumParticles()):
params = drude.getParticleParameters(i)
drudeMap[params[1]] = params[0]
for atom1, atom2 in bondIndices:
drude1 = drudeMap[atom1] if atom1 in drudeMap else None
drude2 = drudeMap[atom2] if atom2 in drudeMap else None
if drude1 is not None:
bondIndices.append((drude1, atom2))
if drude2 is not None:
bondIndices.append((drude1, drude2))
if drude2 is not None:
bondIndices.append((atom1, drude2))
nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale)
parsers["NonbondedForce"] = NonbondedGenerator.parseElement
......@@ -989,7 +1019,7 @@ class GBSAOBCGenerator:
generator = existing[0]
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['scale']))
for t in types[0]:
generator.typeMap[t] = values
......@@ -1046,7 +1076,7 @@ class GBVIGenerator:
ff._forces.append(generator)
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['gamma']))
for t in types[0]:
generator.typeMap[t] = values
......@@ -1129,7 +1159,7 @@ class CustomBondGenerator:
generator.perBondParams.append(param.attrib['name'])
for bond in element.findall('Bond'):
types = ff._findAtomTypes(bond, 2)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.paramValues.append([float(bond.attrib[param]) for param in generator.perBondParams])
......@@ -1177,7 +1207,7 @@ class CustomAngleGenerator:
generator.perAngleParams.append(param.attrib['name'])
for angle in element.findall('Angle'):
types = ff._findAtomTypes(angle, 3)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.types3.append(types[2])
......@@ -1238,11 +1268,11 @@ class CustomTorsionGenerator:
generator.perTorsionParams.append(param.attrib['name'])
for torsion in element.findall('Proper'):
types = ff._findAtomTypes(torsion, 4)
if types is not None:
if None not in types:
generator.proper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
for torsion in element.findall('Improper'):
types = ff._findAtomTypes(torsion, 4)
if types is not None:
if None not in types:
generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
......@@ -1329,7 +1359,7 @@ class CustomGBGenerator:
generator.perParticleParams.append(param.attrib['name'])
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
values = [float(atom.attrib[param]) for param in generator.perParticleParams]
for t in types[0]:
generator.typeMap[t] = values
......@@ -1431,7 +1461,7 @@ class AmoebaBondGenerator:
forceField._forces.append(generator)
for bond in element.findall('Bond'):
types = forceField._findAtomTypes(bond, 2)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.length.append(float(bond.attrib['length']))
......@@ -1544,7 +1574,7 @@ class AmoebaAngleGenerator:
forceField._forces.append(generator)
for angle in element.findall('Angle'):
types = forceField._findAtomTypes(angle, 3)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -2029,7 +2059,7 @@ class AmoebaTorsionGenerator:
for torsion in element.findall('Torsion'):
types = forceField._findAtomTypes(torsion, 4)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -2140,7 +2170,7 @@ class AmoebaPiTorsionGenerator:
for piTorsion in element.findall('PiTorsion'):
types = forceField._findAtomTypes(piTorsion, 2)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.k.append(float(piTorsion.attrib['k']))
......@@ -2259,7 +2289,7 @@ class AmoebaTorsionTorsionGenerator:
for torsionTorsion in element.findall('TorsionTorsion'):
types = forceField._findAtomTypes(torsionTorsion, 5)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -2496,7 +2526,7 @@ class AmoebaStretchBendGenerator:
for stretchBend in element.findall('StretchBend'):
types = forceField._findAtomTypes(stretchBend, 3)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -2653,7 +2683,7 @@ class AmoebaVdwGenerator:
for atom in element.findall('Vdw'):
types = forceField._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
values = [float(atom.attrib['sigma']), float(atom.attrib['epsilon']), float(atom.attrib['reduction'])]
......@@ -2926,7 +2956,7 @@ class AmoebaMultipoleGenerator:
for atom in element.findall('Multipole'):
types = forceField._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
# k-indices not provided default to 0
......@@ -2983,7 +3013,7 @@ class AmoebaMultipoleGenerator:
for atom in element.findall('Polarize'):
types = forceField._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
classIndex = atom.attrib['type']
polarizability = float(atom.attrib['polarizability'])
......@@ -3511,7 +3541,7 @@ class AmoebaWcaDispersionGenerator:
for atom in element.findall('WcaDispersion'):
types = forceField._findAtomTypes(atom, 1)
if types is not None:
if None not in types:
values = [float(atom.attrib['radius']), float(atom.attrib['epsilon'])]
for t in types[0]:
......@@ -3855,7 +3885,7 @@ class AmoebaUreyBradleyGenerator:
forceField._forces.append(generator)
for bond in element.findall('UreyBradley'):
types = forceField._findAtomTypes(bond, 3)
if types is not None:
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -3899,3 +3929,87 @@ class AmoebaUreyBradleyGenerator:
parsers["AmoebaUreyBradleyForce"] = AmoebaUreyBradleyGenerator.parseElement
#=============================================================================================
## @private
class DrudeGenerator:
"""A DrudeGenerator constructs a DrudeForce."""
def __init__(self):
self.typeMap = {}
@staticmethod
def parseElement(element, ff):
existing = [f for f in ff._forces if isinstance(f, DrudeGenerator)]
if len(existing) == 0:
generator = DrudeGenerator()
ff._forces.append(generator)
else:
# Multiple <DrudeForce> tags were found, probably in different files. Simply add more types to the existing one.
generator = existing[0]
for particle in element.findall('Particle'):
types = ff._findAtomTypes(particle, 5)
if None not in types[:2]:
aniso12 = 0.0
aniso34 = 0.0
if 'aniso12' in particle.attrib:
aniso12 = float(particle.attrib['aniso12'])
if 'aniso34' in particle.attrib:
aniso34 = float(particle.attrib['aniso34'])
values = (types[1], types[2], types[3], types[4], float(particle.attrib['charge']), float(particle.attrib['polarizability']), aniso12, aniso34, float(particle.attrib['thole']))
for t in types[0]:
generator.typeMap[t] = values
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
force = mm.DrudeForce()
if not any(isinstance(f, mm.NonbondedForce) for f in sys.getForces()):
raise ValueError('<DrudeForce> must come after <NonbondedForce> in XML file')
# Add Drude particles.
drudeMap = {}
parentMap = {}
for atom in data.atoms:
t = data.atomType[atom]
if t in self.typeMap:
# Find other atoms in the residue that affect the Drude particle.
p = [-1, -1, -1, -1]
values = self.typeMap[t]
for atom2 in atom.residue.atoms():
type2 = data.atomType[atom2]
if type2 in values[0]:
p[0] = atom2.index
elif values[1] is not None and type2 in values[1]:
p[1] = atom2.index
elif values[2] is not None and type2 in values[2]:
p[2] = atom2.index
elif values[3] is not None and type2 in values[3]:
p[3] = atom2.index
drudeIndex = force.addParticle(atom.index, p[0], p[1], p[2], p[3], values[4], values[5], values[6], values[7])
drudeMap[atom.index] = p[0]
parentMap[p[0]] = (atom.index, drudeIndex)
sys.addForce(force)
def postprocessSystem(self, sys, data, args):
# For every nonbonded exclusion between Drude particles, add a screened pair.
drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)][0]
nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
particleMap = {}
for i in range(drude.getNumParticles()):
particleMap[drude.getParticleParameters(i)[0]] = i
for i in range(nonbonded.getNumExceptions()):
(particle1, particle2, charge, sigma, epsilon) = nonbonded.getExceptionParameters(i)
if charge == 0 and epsilon == 0:
# This is an exclusion.
if particle1 in particleMap and particle2 in particleMap:
# It connects two Drude particles, so add a screened pair.
drude1 = particleMap[particle1]
drude2 = particleMap[particle2]
type1 = data.atomType[data.atoms[drude1]]
type2 = data.atomType[data.atoms[drude2]]
thole1 = self.typeMap[type1][8]
thole2 = self.typeMap[type2][8]
drude.addScreenedPair(drude1, drude2, thole1+thole2)
parsers["DrudeForce"] = DrudeGenerator.parseElement
\ No newline at end of file
wrappers/python/simtk/openmm/app/modeller.py
View file @ c5ad2202
......@@ -34,7 +34,7 @@ __author__ = "Peter Eastman"
__version__ = "1.0"
from simtk.openmm.app import Topology, PDBFile, ForceField
from simtk.openmm.app.forcefield import HAngles, _createResidueSignature, _matchResidue
from simtk.openmm.app.forcefield import HAngles, _createResidueSignature, _matchResidue, DrudeGenerator
from simtk.openmm.app.topology import Residue
from simtk.openmm.vec3 import Vec3
from simtk.openmm import System, Context, NonbondedForce, VerletIntegrator, LocalEnergyMinimizer
......@@ -817,6 +817,15 @@ class Modeller(object):
bondedToAtomNoEP[atom1.index].add(atom2.index)
bondedToAtomNoEP[atom2.index].add(atom1.index)
# If the force field has a DrudeForce, record the types of Drude particles and their parents since we'll
# need them for picking particle positions.
drudeTypeMap = {}
for force in forcefield._forces:
if isinstance(force, DrudeGenerator):
for type in force.typeMap:
drudeTypeMap[type] = force.typeMap[type][0]
# Create the new Topology.
newTopology = Topology()
......@@ -894,6 +903,12 @@ class Modeller(object):
position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
elif site.type == 'outOfPlane':
position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
if position is None and atom.type in drudeTypeMap:
# This is a Drude particle. Put it on top of its parent atom.
for atom2, pos in zip(template.atoms, templateAtomPositions):
if atom2.type in drudeTypeMap[atom.type]:
position = deepcopy(pos)
if position is None:
# We couldn't figure out the correct position. As a wild guess, just put it at the center of the residue
# and hope that energy minimization will fix it.
......
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