Irfan Alibay

For your first question about the softcore formalism, we need a bit of time to chat with some folks from the OpenFE TAC.

Thanks for opening this @palominohernandez GAFF support was temporarily removed in openmmforcefields 0.13.0 due to some issues with ambertools, as far as we know the developers are looking into ways...

Thanks @palominohernandez - unfortunately I don't think we've ever tested out simulations with the opc models. My initial thought here is that openmm.Modeller.addSolvent just doesn't support it properly yet (hence...

@jthorton can I take from this that a locally modified version of that xml works?

pinging @hannahbaumann

@richardjgowers it's a "partially us" problem, as you say SDFs don't set Monomerinfo, so we don't propagate the residue name through (so OpenFF / OpenMM just set it to UNK)....

Related: https://github.com/OpenFreeEnergy/gufe/issues/327

@JenkeScheen can you confirm what version of Kartograf you are using?

Cheers @JenkeScheen, thanks for the report. We'll have a quick stab at this a bit later today / over the next few days - there are filters in place for...

@orbeckst I might either take over or overwrite this PR later today - I had started working on my own update earlier.