BioSimSpace.Parameters.gaff(molecule, work_dir=None, net_charge=None, charge_method='BCC', ensure_compatible=True, property_map={}, **kwargs)[source]#

Parameterise using the GAFF force field.

  • molecule (Molecule, str) – The molecule to parameterise, either as a Molecule object or SMILES string.

  • net_charge (int, Charge) – The net charge on the molecule.

  • charge_method (str) – The method to use when calculating atomic charges: “RESP”, “CM2”, “MUL”, “BCC”, “ESP”, “GAS”

  • ensure_compatible (bool) – Whether to ensure that the topology of the parameterised molecule is compatible with that of the original molecule. An exception will be raised if this isn’t the case, e.g. if atoms have been added. When True, the parameterised molecule will preserve the topology of the original molecule, e.g. the original atom and residue names will be kept.

  • work_dir (str) – The working directory for the process.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }


molecule – The parameterised molecule.

Return type: