Test offpele with complex non-standard residues

[martimunicoy]

Description

Let's see how OpenFF works when parameterizing a set of cofactors / prosthetic groups

Solution

@SergiR1996 could provide several examples of compounds to test. It would also be nice to rely on QM calculations for these compounds to use as reference when checking the resulting forcefield parameters.

[SergiR1996]

I have one system involving a covalent bound cofactor, aromatic ammonia-lyases (3,5-dihydro-5-methyldiene-4H-imidazol-4-one, the name of the cofactor). I made some PELE simulations regarding this system with this cofactor and the ligand.

The main problem of using PlopRotTemp to parametrize the cofactor is that you must add dummy terminal hydrogens to have a valid Lewis structure, and then, modify manually the created force field file. I would like that the process of parametrizing this type of cofactors / prosthetic groups became easier.

I attach you this system (the MAE file of the ligand and the PDB structure of the protein with the cofactor), plus the default and the manually modified force field file:

Cofactor_system_example_force_field_file.zip