Add covalent ligand topology in CHARMM36

GROMACS version: 2022
GROMACS modification: Yes
I am trying to add a “new residue” in CHARMM36 force field. This residue is a modified serine with a ligand covalently bound. SO, I created the topology in CgenFF and added it in the force field files, modifying atomtypes.dat, aminoacids.rtp, ffbonded.itp, aminoacids.r2b and residuetypes.dat.

But somehow pdb2gmx is still not recognizing my modifications and saying that cannot find the topology of the residue in the topology database.

I rceated a new residue in aminoacids.rtp and kept the information from the SER and added the correspondents for the ligand as being connected.

DOes somebody have any idea on how to fix this?

Dear Natalia,

without any details on the modifications you did, and the exact output of the pdb2gmx command, this community can give little help. Could you please be more specific?

Also please check that you select the correct FF directory with pdb2gmx (first question / -ff command line switch).