AmberPrmtopFile

class openmm.app.amberprmtopfile.AmberPrmtopFile(file, periodicBoxVectors=None, unitCellDimensions=None)

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

__init__(file, periodicBoxVectors=None, unitCellDimensions=None)

Load a prmtop file.

filestr

the name of the file to load

periodicBoxVectorstuple of Vec3=None

the vectors defining the periodic box

unitCellDimensionsVec3=None

the dimensions of the crystallographic unit cell. For non-rectangular unit cells, specify periodicBoxVectors instead.

Methods

__init__(file[, periodicBoxVectors, …])

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), 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

the newly created System

Return type

System