How to keep S atom unprotonated in pdb2gmx?

User discussions
1

GROMACS version:2023.1
GROMACS modification: No
The target simulation system contains two deprotonated CYS residues and I hope to build the topology for this system using pdb2gmx. All other residues of this protein have been protonated normally, and I am pretty sure that -ignh was not used. My pdb2gmx command worked, but the resulting topology still protonated the target CYSs.

Is there any way to construct deprotonated CYS? Thank you!

PDB2GMX command I use:

gmx pdb2gmx -f protein_H.pdb -o protein_processed.gro -water spc -missing
2

Try without the -missing option. It usually risky to use:
... the use of the option -missing is almost always inappropriate. The -missing option should only be used to generate specialized topologies for amino acid-like molecules to take advantage of rtp entries. If you find yourself using -missing in order to generate a topology for a protein or nucleic acid, don’t; the topology produced is likely physically unrealistic. (Common errors when using GROMACS - GROMACS 2024.3 documentation)

3

Thanks for your suggestion!

gmx pdb2gmx -f protein_H.pdb -o protein_processed.gro -water spc

This instruction also resulted in protonated CYSs.

I am considering whether I need to treat this CYS as a special residue and perform vibrational analysis on it using Gaussian. This would be somewhat troublesome, so I am wondering if there are any simple solution.

4

I would have thought that the protonation states would be untouched in that case. But apparently I was wrong.