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Gallicchio-Lab / openmm-atmmetaforce-plugin

An OpenMM plugin that implements the Alchemical Transfer Potential
GNU Lesser General Public License v2.1
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Examples & Docmentation to run this for RBFE calculation from docked structures #2

Closed JSLJ23 closed 1 year ago

JSLJ23 commented 2 years ago

Hi developers of openmm-atm,

I was wondering if there was any available documentation / example code of how to run a RBFE for docked ligands against a PDB with a known co-cystal structure and ground truth affinity value. I have some structures of ligand SDF files that were docked against a protein with a known hit and Kd/i values and I was hoping to run this to get predictions of binding energies of those docked ligands with respect to a known ground truth.

Thank you.

egallicc commented 2 years ago

Use the AToM-OpenMM middleware. The CDK2 example is probably a good starting point for your purpose.

JSLJ23 commented 1 year ago

Ahh ok thank you, I'll look at the ABFE examples there :)