CGenFF ERROR - attype warning: unknown sulfur type (SD) not supported; skipped molecule

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GROMACS version:
GROMACS modification: Yes/No

Hello everyone,
I want to obtain the topology file for the ligand S-Adenosyl Methionine (SAM) (image attached). While using CGenFF, I am getting the following error.

CHARMM General Force Field (CGenFF) program version 4.0
released June 2024
Copyright (C) 2020 SilcBio LLC
and University of Maryland, School of Pharmacy. All Rights Reserved.

Licensed to:
cgenff server
serverncgenff

License expires: Tue Dec 31 00:00:00 2030

readpar debug: read 683 bonds, 2501 angles, 7460 dihedrals, 203 impropers
and 375437 characters worth of comments.
Now processing molecule SAM …
ringper debug: stored 5-membered ring in stage 1.
ringper debug: stored 6-membered ring in stage 2.
ringper debug: stored 5-membered ring in stage 2.
ringper debug: added anchor for 5-membered ring in stage 2.
ringper debug: added anchor for 6-membered ring in stage 2.
resonance debug: found better resonance chain with
charge -1 ( 0 positive and 1 negative centers) and 1 potential aromatic rings
resonance debug: found resonance chain with
charge -1 ( 0 positive and 1 negative centers) and 1 potential aromatic rings
resonance debug: found perfect resonance chain with
charge 0 ( 0 positive and 0 negative centers) and 0 potential aromatic rings
attype warning: unknown sulfur type (SD) not supported;
skipped molecule.

I have tried changing the atomname of Sulphur to SD, SG, SDP, S, etc., based on the files cgenff.rtp and toppar_all36_prot_na_combined.str, however, in each case, “unknown sulfur type” is reported as error.

While using swissparam, the following error was obtained.
Thank you for using SwissParam.

Unfortunately, topology and parameters were not successfully generated for SAM_withH .
A failure report can be found below.

Failure report:

Possible problem with molecular topology in SAM_withH.mol2.
SwissParam will try to reconstruct the topology from coordinates only.

Topology and parameters were NOT generated. Please check the validity of your molecule.

  • Are all hydrogens present in the mol2 file?
  • Is the mol2 file correct? Please, read “How to obtain a correct mol2 file?” in the www.swissparam.ch website.

SAM
SAM709×341 41.7 KB

Please help me to solve this issue. Should I use GAFF instead? I want to simulate a protein-ligand complex using charmm36 july22 ff.

2

S-adenoylmethionine is already part of the CHARMM36 force field. You do not need to generate a topology yourself; just use pdb2gmx (although you will have to correct the atom names that you have shown in the image because they do not correspond to the FF nomenclature).