BioSimSpace.Parameters.ff99SB(molecule, tolerance=1.2, max_distance=6.0000 A, water_model=None, leap_commands=None, bonds=None, ensure_compatible=True, work_dir=None, property_map={})#

Parameterise a molecule using the named AMBER force field.

  • 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.

  • 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.

  • 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” }


molecule – The parameterised molecule.

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