""" armberprmtopfile.py: Used for loading AMBER prmtop files. This is part of the OpenMM molecular simulation toolkit originating from Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. See https://simtk.org. Portions copyright (c) 2012 Stanford University and the Authors. Authors: Peter Eastman Contributors: Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ __author__ = "Peter Eastman" __version__ = "1.0" from simtk.openmm.app import Topology from simtk.openmm.app import PDBFile from simtk.openmm.app.internal import amber_file_parser import forcefield as ff import element as elem import simtk.unit as unit import simtk.openmm as mm # Enumerated values for implicit solvent model class HCT(object): def __repr__(self): return 'HCT' HCT = HCT() class OBC1(object): def __repr__(self): return 'OBC1' OBC1 = OBC1() class OBC2(object): def __repr__(self): return 'OBC2' OBC2 = OBC2() class GBn(object): def __repr__(self): return 'GBn' GBn = GBn() class GBn2(object): def __repr__(self): return 'GBn2' GBn2 = GBn2() class AmberPrmtopFile(object): """AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it.""" def __init__(self, file): """Load a prmtop file.""" top = Topology() ## The Topology read from the prmtop file self.topology = top self.elements = [] # Load the prmtop file prmtop = amber_file_parser.PrmtopLoader(file) self._prmtop = prmtop # Add atoms to the topology PDBFile._loadNameReplacementTables() lastResidue = None c = top.addChain() for index in range(prmtop.getNumAtoms()): resNumber = prmtop.getResidueNumber(index) if resNumber != lastResidue: lastResidue = resNumber resName = prmtop.getResidueLabel(iAtom=index).strip() if resName in PDBFile._residueNameReplacements: resName = PDBFile._residueNameReplacements[resName] r = top.addResidue(resName, c) if resName in PDBFile._atomNameReplacements: atomReplacements = PDBFile._atomNameReplacements[resName] else: atomReplacements = {} atomName = prmtop.getAtomName(index).strip() if atomName in atomReplacements: atomName = atomReplacements[atomName] # Get the element from the prmtop file if available if prmtop.has_atomic_number: try: element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index])) except KeyError: element = None else: # Try to guess the element from the atom name. upper = atomName.upper() if upper.startswith('CL'): element = elem.chlorine elif upper.startswith('NA'): element = elem.sodium elif upper.startswith('MG'): element = elem.magnesium else: try: element = elem.get_by_symbol(atomName[0]) except KeyError: element = None top.addAtom(atomName, element, r) self.elements.append(element) # Add bonds to the topology atoms = list(top.atoms()) for bond in prmtop.getBondsWithH(): top.addBond(atoms[bond[0]], atoms[bond[1]]) for bond in prmtop.getBondsNoH(): top.addBond(atoms[bond[0]], atoms[bond[1]]) # Set the periodic box size. if prmtop.getIfBox(): top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer) def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer, constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005): """Construct an OpenMM System representing the topology described by this prmtop file. Parameters: - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME. - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions - constraints (object=None) Specifies which bonds angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles. - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument - implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2. - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model. - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model. - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same. - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME. Returns: the newly created System """ methodMap = {ff.NoCutoff:'NoCutoff', ff.CutoffNonPeriodic:'CutoffNonPeriodic', ff.CutoffPeriodic:'CutoffPeriodic', ff.Ewald:'Ewald', ff.PME:'PME'} if nonbondedMethod not in methodMap: raise ValueError('Illegal value for nonbonded method') if not self._prmtop.getIfBox() and nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME): raise ValueError('Illegal nonbonded method for a non-periodic system') constraintMap = {None:None, ff.HBonds:'h-bonds', ff.AllBonds:'all-bonds', ff.HAngles:'h-angles'} if constraints is None: constraintString = None elif constraints in constraintMap: constraintString = constraintMap[constraints] else: raise ValueError('Illegal value for constraints') if implicitSolvent is None: implicitString = None elif implicitSolvent is HCT: implicitString = 'HCT' elif implicitSolvent is OBC1: implicitString = 'OBC1' elif implicitSolvent is OBC2: implicitString = 'OBC2' elif implicitSolvent is GBn: implicitString = 'GBn' elif implicitSolvent is GBn2: implicitString = 'GBn2' else: raise ValueError('Illegal value for implicit solvent model') sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff, nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString, soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater, elements=self.elements) if hydrogenMass is not None: for atom1, atom2 in self.topology.bonds(): if atom1.element == elem.hydrogen: (atom1, atom2) = (atom2, atom1) if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None): transferMass = hydrogenMass-sys.getParticleMass(atom2.index) sys.setParticleMass(atom2.index, hydrogenMass) sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass) for force in sys.getForces(): if isinstance(force, mm.NonbondedForce): force.setEwaldErrorTolerance(ewaldErrorTolerance) if removeCMMotion: sys.addForce(mm.CMMotionRemover()) return sys