Pdb2gmx does not recognize disulfides accurately

GROMACS version: 2022.3
GROMACS modification: No
Dear GROMACS users,

I have a protein-protein complex with seven disulfide bonds and a free cysteine. However, pdb2gmx only recognizes four of the disulfides and leaves the other three as free cysteine. I know this is the case as the disulfides lack the HG atom and have the S-S bond parameterized under [ bonds ] in the topology file, whereas the free cysteines do not. Is there any way around this? Maybe by changing the name of Cys residues in the input pdb?

Arash Firouzbakht

did you try to assign S-S manually by using the option -ss in gmx pdb2gmx ?
Also if you have S-S bridge between different chains, you may need to use also the option -merge.
I hope it helps


using -merge actually took care of one of missing disulfides! For the other ones, it says in the manual that the S-S distance needs to be within 10% of the specified bond length for S-S in specbond.dat (2Å ± 0.2Å). Since my structures are generated by AlphaFold, some of the disulfides were a bit shorter than the cutoff so pdb2gmx left them as free Cys. I am now trying to fix the bond lengths and relax the structure after that.