BioSimSpace.Metadynamics.CollectiveVariable.makeFunnel

BioSimSpace.Metadynamics.CollectiveVariable.makeFunnel(system, protein=None, ligand=None, alpha_carbon_name='CA', property_map={})

Calculate the two sets of atom indices, atoms0 and atoms1, that are used to define the funnel collective variable.

Parameters

• system (System) – The system of interest. This is assumed to be a solvated protein-ligand system.

• protein (Molecule, int) – The protein molecule. This can either be a Molecule object, or the index of the protein within the passed system. If None is passed then we assume that the protein is the largest molecule in the system.

• ligand (Molecule, int, Coordinate) – The ligand molecule. This can either be a Molecule object, the index of the ligand within the passed system, or the position of the binding site within the protein. If None is passed then we assume that the ligand is the second largest molecule in the system.

• alpha_carbon_name (str) – The name of alhpa carbon atoms in the system topology.

• 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

• atoms0 ([int]) – A list of atom indices that define the origin of the funnel.

• atoms1 ([int]) – A list of atom indices that define the inflection point of the funnel.