[Draft] Self-consistently parameterize protein-ligand with espaloma-0.3.0

[kntkb]

Description

This PR is a draft to self-consistently parameterize protein-ligand systems with espaloma-0.3.0 which was built on top of perses-0.10.1. Note that this PR is not ready to be merged to the latest release but intended to keep track of how one could self-consistently parameterize a protein-ligand systems with espaloma-0.3.0.

Motivation and context

Current implementation of perses cannot parameterize the protein-ligand system self-consistently with espaloma. One work around is to parameterize the system with the current implementation (protein: Amber, ligand: espaloma), and use the solvated system to regenerate the protein with EspalomaTemplateGenerator implemented in openmmforcefields.generators.

A more simple way is to handle the protein as a single residue openff.topology.Molecule object and append it with the other small molecules, Then load the list of Molecules into openmmforcefields.generators.SystemGenerator. However, this raised some issues described here.

How has this been tested?

This version was used to run the custom PL-benchmark described here.

[ijpulidos]

Thanks for this @kntkb ! This will help ups come up with the changes we need to be doing in our API to be able to parametrize receptors/proteins as well.