examples on running protein-ligand relative binding calculations

Hey @here,

Are there some examples of how to run protein-ligand relative binding calculations using perses without neq-switching? Only use the equilibrium alchemical simulations. I have two small-molecule .sdf files and one protein .pdb file. Both molecules have been aligned together based on the common core atom mapping.

Thanks!

Best, Pengfei

[jchodera]

The Perses heavily depends on the openeye. I do not have the license of openeye. Could it be replaced by the open-source packages e.g. rdkit, openbabel et al?

Replacing OpenEye toolkit dependencies with the Open Force Field Toolkit—which provides an abstraction layer to multiple toolkits, including the open source RDKit—is on our roadmap, but it is not urgent for the folks funding development at the moment.

I have one scenario where I have the AMBER prmtop and inpcrd files including both aligned together ligand topology and positions. Are there quick ways to run protein-ligand binding using perses? Thanks!

This is not currently on our roadmap, but if you like, you could submit a feature request where you would specify prmtop/inpcrd files for each state and have perses run a free energy calculation. I can’t guarantee when we would be able to get to this due to very limited development resources, however.

[ijpulidos]

Hi @freeenergylab , we do have an example for such a system in the examples/protein-ligand/cli which you could run with something like perses-relative ani.yaml. You might want to to give that a shot.

We do have to make the documentation clearer on these examples. We will work on that. Hope this works.