peleffy.forcefield.OpenFFOPLS2005ForceField

class peleffy.forcefield.OpenFFOPLS2005ForceField(forcefield_name)

It defines an hybrid force field from the combination of OpenFF and OPLS2005.

__init__(forcefield_name)

It initializes the OpenFFOPLS2005ForceField class.

Parameters

openff_name (str) – The name of the OpenFF forcefield to employ

Examples

Load a molecule and generate its parameters with an hybrid OpenFF-OPLS2005 force field

>>> from peleffy.topology import Molecule

>>> molecule = Molecule('molecule.pdb')

>>> from peleffy.forcefield import OpenFFOPLS2005ForceField

>>> hybridff = OpenFFOPLS2005ForceField('openff_unconstrained-1.2.1.offxml')
>>> parameters = hybridff.parameterize(molecule)

We can customized it by selecting which force field employ for each parameter type. For example, below we are parameterizing all force field elements with OPLS2005 except for the dihedrals

>>> from peleffy.topology import Molecule

>>> molecule = Molecule('molecule.pdb')

>>> from peleffy.forcefield import OpenFFOPLS2005ForceField

>>> hybridff = OpenFFOPLS2005ForceField('openff_unconstrained-1.2.1.offxml')

>>> hybridff.set_nonbonding_parameters('OPLS2005')
>>> hybridff.set_bond_parameters('OPLS2005')
>>> hybridff.set_angle_parameters('OPLS2005')
>>> hybridff.set_dihedral_parameters('OpenFF')

>>> parameters = hybridff.parameterize(molecule)

parameterize(molecule, charge_method=None)

It parameterizes the supplied molecule.

Parameters

• molecule (a peleffy.topology.Molecule) – The peleffy’s Molecule object to parameterize

• charge_method (str) – The name of the charge method to employ

Returns

parameters – The parameter wrapper containing the parameters generated with the current force field

Return type

a peleffy.forcefield.parameters.BaseParameterWrapper object

set_angle_parameters(selection)

It sets which force field to use to assign parameters to angles.

Parameters

selection (str) – The force field to employ. One of (‘OpenFF’, ‘OPLS2005’)

set_bond_parameters(selection)

It sets which force field to use to assign parameters to bonds.

Parameters

selection (str) – The force field to employ. One of (‘OpenFF’, ‘OPLS2005’)

set_dihedral_parameters(selection)

It sets which force field to use to assign parameters to dihedrals.

Parameters

selection (str) – The force field to employ. One of (‘OpenFF’, ‘OPLS2005’)

set_nonbonding_parameters(selection)

It sets which force field to use to assign nonbonding parameters. Nonbonding parameters are: ‘atom_types’, ‘sigmas’, ‘epsilons’, ‘SGB_radii’, ‘vdW_radii’, ‘gammas’, ‘alphas’, ‘GBSA_radii’ and ‘GBSA_scales’.

Parameters

selection (str) – The force field to employ. One of (‘OpenFF’, ‘OPLS2005’)

Attributes

name	It returns the name of the force field.
parameters	It returns the parameters obtained with the force field.
type	It returns the type of the force field.