pysimm.amber

Module Contents

Functions

cleanup_antechamber()	pysimm.amber.cleanup_antechamber
calc_charges(s, charge_method='bcc', cleanup=True)	pysimm.amber.calc_charges
get_forcefield_types(s, types='gaff', f=None)	pysimm.amber.get_forcefield_types

Attributes

ANTECHAMBER_EXEC

pysimm.amber.ANTECHAMBER_EXEC

pysimm.amber.cleanup_antechamber()

pysimm.amber.cleanup_antechamber

Removes temporary files created by antechamber and pysimm.

Parameters

None –

Returns

None

pysimm.amber.calc_charges(s, charge_method='bcc', cleanup=True)

pysimm.amber.calc_charges

Calculates charges using antechamber. Defaults to am1-bcc charges.

Parameters

• s – System for which to calculate charges. System object is updated in place

• charge_method – name of charge derivation method to use (default: bcc)

• cleanup – removes temporary files created by antechamber (default: True)

Returns

None

pysimm.amber.get_forcefield_types(s, types='gaff', f=None)

pysimm.amber.get_forcefield_types

Uses antechamber to determine atom types. Defaults to GAFF atom types. Retrieves ParticleType objects from force field is provided

Parameters

• s – System for which to type

• types – name of atom types to use (default: gaff)

• f – forcefield object to retrieve ParticleType objects from if not present in s (default: None)

Returns

None