AmberPrmtopFile

class simtk.openmm.app.amberprmtopfile.AmberPrmtopFile(file)

AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it.

__init__(file)

Load a prmtop file.

Methods

__init__(file)	Load a prmtop file.
createSystem([nonbondedMethod, ...])	Construct an OpenMM System representing the topology described by this prmtop file.

__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__

createSystem(nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), constraints=None, rigidWater=True, implicitSolvent=None, implicitSolventSaltConc=Quantity(value=0.0, unit=mole/liter), implicitSolventKappa=None, temperature=Quantity(value=298.15, unit=kelvin), soluteDielectric=1.0, solventDielectric=78.5, removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005, switchDistance=Quantity(value=0.0, unit=nanometer))

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.
• 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.
• ewaldErrorTolerance (float=0.0005) – The error tolerance to use if nonbondedMethod is Ewald or PME.
• 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

Returns:

the newly created System

Return type:

System