Adding a new residue covalently linked to multiple cysteines

[ganesh7shahane]

GROMACS version: 2024.4
GROMACS modification: No

Hi Gromacs community,

I am trying to setup a simulation of a peptide that is covalently linked via its three cysteines to an aliphatic heterocyclic scaffold (PDB: 6RW2).

A simplistic diagram of this linkage looks like this:

After generating the parameters (.itp) of the scaffold, I added them to the force field’s aminoacids.rtp. In the [bonds] section for the scaffold, I do specify that the carbons of the scaffold are bonded to thiol sulphur (+SG):

  [ bonds ]
    .
    .
    .
   C16    +SG
   C16    H161
   C16    H162
   C19    +SG
   C19    H191
   C19    H192
   C25    +SG
   C25    H251
   C25    H252

However, when I call pdb2gmx on the input PDB file of the peptide to generate the full topology, I get the following error where “29N” is the name of the scaffold:

Fatal error:
Residue 418 named 29N of a molecule in the input file was mapped
to an entry in the topology database, but the atom SG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

The input PDB file of the peptide looks like this, and it does not have SG present in it:

Although SG is present as part of the CYS residue of the peptides:

My question is, how do i resolve the above error, when SG is clearly present in the input file as part of the CYS residues but not as part of the scaffold 29N?