CharmmPsfFile

class simtk.openmm.app.charmmpsffile.CharmmPsfFile(*args, **kwargs)

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

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__(*args, **kwargs)

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

Methods

__init__(*args, **kwargs) 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, unit, beta, unit, ...]) Sets the periodic box boundary conditions.

Attributes

ANGLE_FORCE_GROUP
BOND_FORCE_GROUP
CMAP_FORCE_GROUP
DIHEDRAL_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
topology Create an OpenMM Topology object from the stored bonded network
__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__
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.
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)

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, or PME.
  • 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.
  • ewaldErrorTolerance (float=0.0005) – The error tolerance to use if the nonbonded method is Ewald or PME.
  • flexibleConstraints (bool=True) – Are our constraints flexible or not?
  • verbose (bool=False) – Optionally prints out a running progress report
system

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

boxLengths

Return tuple of 3 units

boxVectors

Return the box vectors

deleteCmap()

Deletes the CMAP terms from the CHARMM PSF