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.
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