pysimm.amber module

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

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.cleanup_antechamber()[source]

Removes temporary files created by antechamber and pysimm.

Parameters:None –
Returns:None
pysimm.amber.get_forcefield_types(s, types='gaff', f=None)[source]

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