2022-03-16 Jang/Thompson Check-in meeting notes

Notebook issues

• HJ – I can’t find the code to make docked.pdb in the notebook.

• MT – Sorry, I made some changes. The most recent version should work.

• HJ – Thanks, it works now.

• JW – You shouldn’t have to delete the ImproperTorsions, or load the 0.0.1

Other macromolecule parameters?

• HJ – Does OpenFF have lipid and nucleic acid parameters?

• JW – No. If we manage to get a neural net to assign charges, then it will be POSSIBLE to parameterize those molecules using our small molecule FFs. But it may not be scientifically advisable. Lipids would probably be OK, but nucleic acids may not behave well.

Ion parameters in OFFXML

• HJ - I see far more metal/ion parameters in

  than I see in Sage

• JW – Those could be trivially ported into an OFFXML. But I don’t think our FF team would agree to do it, so you will need to do it at OpenEye. I’d be happy to check these over.