CharmmPsfFile

class openmm.app.charmmpsffile.CharmmPsfFile(psf_name, periodicBoxVectors=None, unitCellDimensions=None)

A chemical structure instantiated from CHARMM files.

This structure has numerous attributes that are lists of the elements of this structure, including atoms, bonds, torsions, etc. The attributes are

  • residue_list

  • atom_list

  • bond_list

  • angle_list

  • dihedral_list

  • dihedral_parameter_list

  • improper_list

  • cmap_list

  • donor_list # hbonds donors?

  • acceptor_list # hbond acceptors?

  • group_list # list of nonbonded interaction groups

Four additional lists for Drude psf: - drudeconsts_list - drudepair_list - lonepair_list - aniso_list

Additional attribute is available if a CharmmParameterSet is loaded into this structure.

  • urey_bradley_list

The lengths of each of these lists gives the pointers (e.g., natom, nres, etc.)

Examples

>>> cs = CharmmPsfFile("testfiles/test.psf")
>>> len(cs.atom_list)
33
>>> len(cs.bond_list)
32
__init__(psf_name, periodicBoxVectors=None, unitCellDimensions=None)

Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data.

Parameters

  • psf_name (str) – Name of the PSF file (it must exist)

  • periodicBoxVectors (tuple of Vec3) – the vectors defining the periodic box

  • unitCellDimensions (Vec3) – the dimensions of the crystallographic unit cell. For non-rectangular unit cells, specify periodicBoxVectors instead.

:raises IOError : If file “psf_name” does not exist: :raises CharmmPSFError: If any parsing errors are encountered:

Methods

__init__(psf_name[, periodicBoxVectors, …])

Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data.

createSystem(params[, nonbondedMethod, …])

Construct an OpenMM System representing the topology described by the prmtop file.

deleteCmap()

Deletes the CMAP terms from the CHARMM PSF

loadParameters(parmset)

Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files.

setBox(a, b, c[, alpha, beta, gamma])

Sets the periodic box boundary conditions.

Attributes

ANGLE_FORCE_GROUP

BOND_FORCE_GROUP

CMAP_FORCE_GROUP

DIHEDRAL_FORCE_GROUP

DRUDE_FORCE_GROUP

GB_FORCE_GROUP

IMPROPER_FORCE_GROUP

NONBONDED_FORCE_GROUP

UREY_BRADLEY_FORCE_GROUP

boxLengths

Return tuple of 3 units

boxVectors

Return the box vectors

system

Return the cached system class – it needs to be initialized via “createSystem” first!

topology

Create an OpenMM Topology object from the stored bonded network
loadParameters(parmset)

Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files.

Parameters

parmset (CharmmParameterSet) – List of all parameters

Notes

  • If any parameters that are necessary cannot be found, a MissingParameter exception is raised.

  • If any dihedral or improper parameters cannot be found, I will try inserting wildcards (at either end for dihedrals and as the two central atoms in impropers) and see if that matches. Wild-cards will apply ONLY if specific parameters cannot be found.

  • This method will expand the dihedral_parameter_list attribute by adding a separate Dihedral object for each term for types that have a multi-term expansion

setBox(a, b, c, alpha=Quantity(value=90.0, unit=degree), beta=Quantity(value=90.0, unit=degree), gamma=Quantity(value=90.0, unit=degree))

Sets the periodic box boundary conditions.

Parameters

  • a (length) – Lengths of the periodic cell

  • b (length) – Lengths of the periodic cell

  • c (length) – Lengths of the periodic cell

  • alpha (floats, optional) – Angles between the periodic cell vectors.

  • beta (floats, optional) – Angles between the periodic cell vectors.

  • gamma (floats, optional) – Angles between the periodic cell vectors.

property topology

Create an OpenMM Topology object from the stored bonded network

createSystem(params, nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), switchDistance=Quantity(value=0.0, unit=nanometer), constraints=None, rigidWater=True, implicitSolvent=None, implicitSolventKappa=None, implicitSolventSaltConc=Quantity(value=0.0, unit=mole / liter), temperature=Quantity(value=298.15, unit=kelvin), soluteDielectric=1.0, solventDielectric=78.5, removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005, flexibleConstraints=True, verbose=False, gbsaModel=None, drudeMass=Quantity(value=0.4, unit=dalton))

Construct an OpenMM System representing the topology described by the prmtop file. You MUST have loaded a parameter set into this PSF before calling createSystem. If not, AttributeError will be raised. ValueError is raised for illegal input.

Parameters

  • params (CharmmParameterSet) – The parameter set to use to parametrize this molecule

  • 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.

  • switchDistance (distance=0*nanometer) – The distance at which the switching function is active for nonbonded interactions. If the switchDistance evaluates to boolean False (if it is 0), no switching function will be used. Illegal values will raise a ValueError

  • constraints (object=None) – Specifies which bonds or 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, or GBn

  • implicitSolventKappa (float=None) – Debye screening parameter to model salt concentrations in GB solvent.

  • implicitSolventSaltConc (float=0.0*u.moles/u.liter) – Salt concentration for GB simulations. Converted to Debye length kappa

  • temperature (float=298.15*u.kelvin) – Temperature used in the salt concentration-to-kappa conversion for GB salt concentration term

  • 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 the nonbonded method is Ewald, PME, or LJPME.

  • flexibleConstraints (bool=True) – If True, parameters for constrained degrees of freedom will be added to the System

  • verbose (bool=False) – Optionally prints out a running progress report

  • gbsaModel (str=None) – Can be ACE (to use the ACE solvation model) or None. Other values raise a ValueError

  • drudeMass (mass=0.4*amu) – The mass to use for Drude particles. Any mass added to a Drude particle is subtracted from its parent atom to keep their total mass the same.

property system

Return the cached system class – it needs to be initialized via “createSystem” first!

property boxLengths

Return tuple of 3 units

property boxVectors

Return the box vectors

deleteCmap()

Deletes the CMAP terms from the CHARMM PSF