Issue with Zn ion coordination residues in PDBtoPQR

[SavanaMaria]

Hi,
I am trying to generate electrostatic surface maps of a protein that is folded around two Zn ions. Each Zn ion is coordinated by 3 cysteine residues and a histidine residue. Of course, the cysteine residues and one of the nitrogen groups on the histidine can not be protonated in this situation since they are coordinating the Zn ions.

I have a pdb file of this protein where the CYS residues are designated at CYM so they do not protonate. This annotation should be acceptable to use with CHARMM forcefields, however, the PDBtoPQR web server will not accept this annotation and deletes the residues each time I run the PDB file through.

I can manually edit the PDB file to change the instances of CYM to CYS which the pdbtopqr server accepts but then protonates these cysteines. Again, these cysteines can't be protonated as they are coordinating the Zn ions that are present in the structure (notated as HETATM so the pdbtopqr server accepts them). Does anyone have any solution to this issue? I am wholly out of ideas to try.