I'd like to run MD on a protein that has an SAM (S-adenosyl methionine) ligand. The question has come up before (here: http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1980
) and people mentioned that there was a patch somewhere.
In CHARMM36 this patch SAM seems to have disappeared, at least I can't find it anywhere, and cationic tricoordinate sulphur isn't parametrized in cgenff or CHARMM. Does anyone have a topology and parameters?