BioSimSpace.Parameters.ff99(molecule, water_model=None, leap_commands=None, work_dir=None, property_map={})

Parameterise using the ff99 force field.

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

  • water_model (str) – The water model used to parameterise any structural ions. Run ‘BioSimSpace.Solvent.waterModels()’ to see the supported water models. This is ignored if ions are not present.

  • leap_commands ([str]) – An optional list of extra commands for the LEaP program. These will be added after any default commands and can be used to, e.g., load additional parameter files. When this option is set, we can no longer fall back on GROMACS’s pdb2gmx.

  • 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