BioSimSpace.Parameters.ff03

BioSimSpace.Parameters.ff03(molecule, tolerance=1.2, max_distance=6.0000 A, water_model=None, pre_mol_commands=None, post_mol_commands=None, bonds=None, ensure_compatible=True, work_dir=None, property_map={})

Parameterise a molecule using the named AMBER force field.

Parameters:

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

  • tolerance (float) – The tolerance used when searching for disulphide bonds. Atoms will be considered to be bonded if they are a distance of less than tolerance times the sum of the equilibrium bond radii apart.

  • max_distance (Length) – The maximum distance between atoms when searching for disulphide bonds.

  • water_model (str) – The water model used to parameterise any structural ions. Run ‘BioSimSpace.Solvent.waterModels()’ to see the supported water models. This can also be used to parameterise water molecules, or lone oxygen atoms corresponding to structural (crystal) water molecules.

  • pre_mol_commands ([str]) – A list of custom LEaP commands to be executed before loading the molecule. This can be used for loading custom parameter files, or sourcing additional scripts. Make sure to use absolute paths when specifying any external files. When this option is set, we can no longer fall back on GROMACS’s pdb2gmx.

  • post_mol_commands ([str]) – A list of custom LEaP commands to be executed after loading the molecule. This allows the use of additional commands that operate on the molecule, which is named “mol”. When this option is set, we can no longer fall back on GROMACS’s pdb2gmx.

  • bonds (((class:Atom, class:Atom))) – An optional tuple of atom pairs to specify additional atoms that should be bonded.

  • 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. Set this to False is parameterising lone oxygen atoms corresponding to structural (crystal) water molecules. 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” }

Returns:

process – A process to parameterise the molecule in the background. Call the .getMolecule() method on the returned process to block until the parameterisation is complete and get the parameterised molecule.

Return type:

Process