In many systems there are extra non-standard residues that bind along side a ligand. There are (limited) capabilities for handling these within BAC.

Cofactors

The first step is to parameterize the cofactor just as described previously for the ligand. This should provide you with a prep, frcmod and matching PDB file. The prep file then needs to be converted into an Amber lib file. This is done using tLeap and a script similar to the following (you need to edit the filenames to match the prep, frcmod and PDB files you generated):

loadamberprep sam.prep
SAM = loadpdb sam-h.pdb
loadamberparams sam.frcmod
saveoff SAM sam.lib

Now make copies of the lib and frcmod files named COFACTOR.lib and COFACTOR.frcmod.

These should be added to the top level of the tarball containing the ligand parameters. So that for the tarball contents for a cofactor and a ligand called 4ZX would look like:

COFACTOR.lib
COFACTOR.frcmod
4zx/4zx.frcmod
4zx/4zx.prep