def createSystem(self,
nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=1.0 * u.nanometer,
constraints=None,
rigidWater=True,
implicitSolvent=None,
implicitSolventSaltConc=0.0 * (u.moles / u.liter),
implicitSolventKappa=None,
temperature=298.15 * u.kelvin,
soluteDielectric=1.0,
solventDielectric=78.5,
removeCMMotion=True,
hydrogenMass=None,
ewaldErrorTolerance=0.0005,
switchDistance=0.0 * u.nanometer,
gbsaModel='ACE'):
"""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, PME, or LJPME.
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.
implicitSolventSaltConc : float=0.0*unit.moles/unit.liter
The salt concentration for GB calculations (modelled as a debye
screening parameter). It is converted to the debye length (kappa)
using the provided temperature and solventDielectric
temperature : float=300*kelvin
Temperature of the system. Only used to compute the Debye length
from implicitSolventSoltConc
implicitSolventKappa : float units of 1/length
If this value is set, implicitSolventSaltConc will be ignored.
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. If rigidWater is used to make water molecules
rigid, then water hydrogens are not altered.
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
switchDistance : float=0*nanometers
The distance at which the potential energy switching function is
turned on for Lennard-Jones interactions. If the switchDistance is 0
or evaluates to boolean False, no switching function will be used.
Values greater than nonbondedCutoff or less than 0 raise ValueError
gbsaModel : str='ACE'
The SA model used to model the nonpolar solvation component of GB
implicit solvent models. If GB is active, this must be 'ACE' or None
(the latter indicates no SA model will be used). Other values will
result in a ValueError
Returns
-------
System
the newly created System
"""
methodMap = {
ff.NoCutoff: 'NoCutoff',
ff.CutoffNonPeriodic: 'CutoffNonPeriodic',
ff.CutoffPeriodic: 'CutoffPeriodic',
ff.Ewald: 'Ewald',
ff.PME: 'PME',
ff.LJPME: 'LJPME'
}
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, ff.LJPME):
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')
# If implicitSolventKappa is None, compute it from the salt concentration
if implicitSolvent is not None and implicitSolventKappa is None:
if u.is_quantity(implicitSolventSaltConc):
implicitSolventSaltConc = implicitSolventSaltConc.value_in_unit(
u.moles / u.liter)
if u.is_quantity(temperature):
temperature = temperature.value_in_unit(u.kelvin)
# The constant is 1 / sqrt( epsilon_0 * kB / (2 * NA * q^2 * 1000) )
# where NA is avogadro's number, epsilon_0 is the permittivity of
# free space, q is the elementary charge (this number matches
# Amber's kappa conversion factor)
implicitSolventKappa = 50.33355 * sqrt(
implicitSolventSaltConc / solventDielectric / temperature)
# Multiply by 0.73 to account for ion exclusions, and multiply by 10
# to convert to 1/nm from 1/angstroms
implicitSolventKappa *= 7.3
elif implicitSolvent is None:
implicitSolventKappa = 0.0
sys = amber_file_parser.readAmberSystem(
self.topology,
prmtop_loader=self._prmtop,
shake=constraintString,
nonbondedCutoff=nonbondedCutoff,
nonbondedMethod=methodMap[nonbondedMethod],
flexibleConstraints=False,
gbmodel=implicitString,
soluteDielectric=soluteDielectric,
solventDielectric=solventDielectric,
implicitSolventKappa=implicitSolventKappa,
rigidWater=rigidWater,
elements=self.elements,
gbsaModel=gbsaModel)
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == elem.hydrogen:
(atom1, atom2) = (atom2, atom1)
if rigidWater and atom2.residue.name == 'HOH':
continue
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 isinstance(force, (mm.NonbondedForce, mm.CustomNonbondedForce)):
if switchDistance and nonbondedMethod is not ff.NoCutoff:
# make sure it's legal
if (_strip_optunit(switchDistance, u.nanometer) >=
_strip_optunit(nonbondedCutoff, u.nanometer)):
raise ValueError(
'switchDistance is too large compared '
'to the cutoff!')
if _strip_optunit(switchDistance, u.nanometer) < 0:
# Detects negatives for both Quantity and float
raise ValueError(
'switchDistance must be non-negative!')
force.setUseSwitchingFunction(True)
force.setSwitchingDistance(switchDistance)
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
return sys
def createSystem(self,
nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=1.0 * nanometer,
ewaldErrorTolerance=0.0005,
removeCMMotion=True,
hydrogenMass=None,
OPLS=False,
implicitSolvent=None,
AGBNPVersion=1):
"""Construct an OpenMM System representing the topology described by this
DMS file
Parameters
----------
nonbondedMethod : object=NoCutoff
The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
nonbondedCutoff : distance=1*nanometer
The cutoff distance to use for nonbonded interactions
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
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.
OPLS : boolean=False
If True, forces OPLS combining rules
implicitSolvent: string=None
If not None, creates implicit solvent force of the given name
Allowed values are: HCT and 'AGBNP'
(the corresponding tables must be present in the DMS file)
AGBNPVersion: int=1
AGBNP implicit solvent version
"""
self._checkForUnsupportedTerms()
sys = mm.System()
# Build the box dimensions
boxSize = self.topology.getUnitCellDimensions()
if boxSize is not None:
sys.setDefaultPeriodicBoxVectors(
(boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME,
ff.LJPME):
raise ValueError(
'Illegal nonbonded method for a non-periodic system')
# Create all of the particles
for (fcounter, conn, tables, offset) in self._localVars():
for mass in conn.execute('SELECT mass FROM particle ORDER BY id'):
sys.addParticle(mass[0] * dalton)
# Add all of the forces
self._addBondsToSystem(sys)
self._addAnglesToSystem(sys)
self._addConstraintsToSystem(sys)
self._addPeriodicTorsionsToSystem(sys, OPLS)
self._addImproperHarmonicTorsionsToSystem(sys)
self._addCMAPToSystem(sys)
self._addVirtualSitesToSystem(sys)
self._addPositionalHarmonicRestraints(sys)
nb, cnb = self._addNonbondedForceToSystem(sys, OPLS)
# Finish configuring the NonbondedForce.
methodMap = {
ff.NoCutoff: mm.NonbondedForce.NoCutoff,
ff.CutoffNonPeriodic: mm.NonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic: mm.NonbondedForce.CutoffPeriodic,
ff.Ewald: mm.NonbondedForce.Ewald,
ff.PME: mm.NonbondedForce.PME,
ff.LJPME: mm.NonbondedForce.LJPME
}
nb.setNonbondedMethod(methodMap[nonbondedMethod])
nb.setCutoffDistance(nonbondedCutoff)
nb.setEwaldErrorTolerance(ewaldErrorTolerance)
if cnb is not None:
nb.setUseDispersionCorrection(False)
if nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME,
ff.LJPME):
cnb.setNonbondedMethod(methodMap[ff.CutoffPeriodic])
cnb.setCutoffDistance(nonbondedCutoff)
elif nonbondedMethod == ff.CutoffNonPeriodic:
cnb.setNonbondedMethod(methodMap[ff.CutoffNonPeriodic])
cnb.setCutoffDistance(nonbondedCutoff)
else:
cnb.setNonbondedMethod(methodMap[ff.NoCutoff])
cnb.setUseSwitchingFunction(False)
cnb.setUseLongRangeCorrection(False)
#add implicit solvent model.
if implicitSolvent is not None:
if not (implicitSolvent in (HCT, 'AGBNP', 'GVolSA', 'AGBNP3')):
raise ValueError('Illegal implicit solvent method')
if self._verbose:
print('Adding implicit solvent ...')
#with implicit solvent turn off native reaction field
#However note that this does not affect the shifted Coulomb potential of the Nonbonded force
#(it affects the only the energy, not the forces and equation of motion)
nb.setReactionFieldDielectric(1.0)
if implicitSolvent is HCT:
gb_parms = self._get_gb_params()
if gb_parms:
if self._verbose:
print('Adding HCT GB force ...')
gb = GBSAHCTForce(SA='ACE')
for i in range(len(gb_parms)):
gb.addParticle(list(gb_parms[i]))
gb.finalize()
sys.addForce(gb)
else:
raise IOError("No HCT parameters found in DMS file")
if implicitSolvent == 'AGBNP3':
#load AGBNP3 plugin if available
try:
from AGBNP3plugin import AGBNP3Force
except ImportError:
raise NotImplementedError(
'AGBNP3 is not supported in this version')
#sets up AGBNP3
gb_parms = self._get_agbnp2_params()
if gb_parms:
if self._verbose:
print('Adding AGBNP3 force ...')
gb = AGBNP3Force()
# add particles
for i in range(len(gb_parms)):
p = gb_parms[i]
gb.addParticle(p[0], p[1], p[2], p[3], p[4], p[5],
p[6])
# connection table (from bonds)
self._add_agbnp2_ct(gb)
sys.addForce(gb)
else:
raise IOError("No AGBNP parameters found in DMS file")
if implicitSolvent == 'GVolSA':
#implemented as AGBNP version 0
implicitSolvent = 'AGBNP'
AGBNPVersion = 0
if self._verbose:
print('Using GVolSA')
if implicitSolvent == 'AGBNP':
#load AGBNP plugin if available
try:
from AGBNPplugin import AGBNPForce
except ImportError:
raise NotImplementedError(
'AGBNP is not supported in this version')
#sets up AGBNP
gb_parms = self._get_agbnp2_params()
if gb_parms:
gb = AGBNPForce()
gb.setNonbondedMethod(methodMap[nonbondedMethod])
gb.setCutoffDistance(nonbondedCutoff)
gb.setVersion(AGBNPVersion)
if self._verbose:
print('Using AGBNP force version %d ...' %
AGBNPVersion)
# add particles
for i in range(len(gb_parms)):
[
radiusN, chargeN, gammaN, alphaN, hbtype, hbwN,
ishydrogenN
] = gb_parms[i]
h_flag = ishydrogenN > 0
gb.addParticle(radiusN, gammaN, alphaN, chargeN,
h_flag)
sys.addForce(gb)
self.gb_parms = gb_parms
self.agbnp = gb
else:
raise IOError("No AGBNP parameters found in DMS file")
# Adjust masses.
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == hydrogen:
(atom1, atom2) = (atom2, atom1)
if atom2.element == hydrogen and atom1.element not in (
hydrogen, None):
transferMass = hydrogenMass - sys.getParticleMass(
atom2.index)
sys.setParticleMass(atom2.index, hydrogenMass)
sys.setParticleMass(
atom1.index,
sys.getParticleMass(atom1.index) - transferMass)
# Add a CMMotionRemover.
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
return sys