plan-rbfe-network command#

openfe plan-rbfe-network#

Plan a relative binding free energy network, saved as JSON files for the quickrun command.

This tool is an easy way to set up a RBFE calculation campaign. The JSON files this outputs can be used to run each leg of the campaign. For customized setups, please consider using the Python layer of openfe. This tool makes the following choices:

  • Atom mappings performed by LOMAP, with settings max3d=1.0 and element_change=False

  • Minimal spanning network as the network planner, with LOMAP default score as the weight function

  • Water as solvent, with NaCl at 0.15 M.

  • Protocol is the OpenMM-based relative hybrid topology protocol, with default settings.

The generated Network will be stored in a folder containing for each transformation a JSON file, that can be run with quickrun.

openfe plan-rbfe-network [OPTIONS]

Options

-M, --molecules <molecules>#

Required A directory or file containing all molecules to be loaded, either as a single SDF or multiple MOL2/SDFs. Any number of sdf paths.

-p, --protein <protein>#

Required ProteinComponent. Can be provided as an PDB or as a PDBx/mmCIF file. string.

-C, --cofactors <cofactors>#

Path to cofactors sdf file. This may contain multiple molecules

-s, --settings <yaml_settings>#

Path to planning settings yaml file.

-o, --output-dir <output_dir>#

Path to the output directory. Defaults to ./alchemicalNetwork.