An example of using espaloma 0.3 for proteins/protein complexes.

[amin-sagar]

Dear Espaloma developers.

I read the Espaloma 0.3 paper a couple of days ago and it looks awesome.

I have installed Espaloma and ran the example scripts which start from SMILES input.

I regularly do simulations of protein-peptide complexes having non-canonical amino acids. Currently, I parameterize the non-canonical amino acids using mdgx from AmberTools. The section of the paper where the protein-ligand simulations were done using Espaloma for both protein and ligand indicates that Espaloma could be a really nice alternative.

Currently, I don't have an openeye license so I can't do FEP calculations using PERSES.

I was looking for any examples where the protein was also parameterized using Espaloma but without using PERSES.
I have found the script at
https://github.com/kntkb/perses/blob/0d069fc1cf31b8cce1ae7a1482c3fa46bc1382d2/perses/app/relative_setup.py#L883
and I am trying to adapt it for my use but I am very new to the openmm/openff ecosystem.

It would be great if someone can share an example script for using Espaloma for a protein or protein complex system.

Best,
Amin.