AmberPrmtopFile Class Reference

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

List of all members.

Public Member Functions
def	__init__
	Load a prmtop file.
def	createSystem
	Construct an OpenMM System representing the topology described by this prmtop file.
Public Attributes
	topology
	The Topology read from the prmtop file.
	elements

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Detailed Description

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

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Constructor & Destructor Documentation

def __init__	(		self,
			file
	)

Load a prmtop file.

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Member Function Documentation

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
	)

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:

(System) the newly created System

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Member Data Documentation

elements

topology

The Topology read from the prmtop file.

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The documentation for this class was generated from the following file:

• amberprmtopfile.py