Generate Protein - Ligand System

[entropybit]

Hi,

I am wondering what would be a clean way to create a protein ligand system where the ligand is parametrized with one of the MLFFs ?

In the example it is shown how to create a mixed system but this requires already having a topology + system parametrized without the MLFF. Currently I am trying to do this by just creating a mixed system using one of the small molecule FFs together with e.g. amber. So I get a system where my Protein is parametrized with amber and the Ligand with the small molecule FF. I can then use this system and topology together with a list of atom ids for the ligand to use the mixed system functionality from openmm-ml but this seems very messy.

Is there a better way, or am I maybe doing something horribly wrong in this approach to start with ?