Adding custom residues/molecules to OpenMM force fields

[Brian Geiss]

I am interested in adding phosphorylated residues (serines/threonines/tyrosines) and other ligands (GTP/SAH) (http://www.pharmacy.manchester.ac.uk/bryce/amber) to my simulations in OpenMM. Is there a guide or instructions for updating the .xml force field files OpenMM uses to add new parameters? I've never modified a force field before so I'm not quite sure what to do, but I need some of these additional molecules to do simulations in OpenMM that I'm interested in.

Thank you in advance for any help.

Best,

-Brian

[Joy Ku]

Hi Brian,

I think the OpenMM application guide has the information you're looking for. Chapter 6 is titled "Creating Force Fields." Note that this is in the application guide, not the users guide - two different documents.

Joy

[Brian Geiss]

Hi Joy,

Serves me right for not reading the instruction manual... ;') Are there any plans on having a repository for extended OpenMM forcefields or ligand/solvent parameters in the xml format since it's different than is used by other programs?

Best,

-Brian

[Joy Ku]

Yes, we are planning on a repository both for example scripts and extended OpenMM forcefields. We will share the news here and through the OpenMM mailing list once they have been set up.

Joy