I am using the PMX tool to generate a hybrid (dual) topology file for proteins. When I do mutation of uncharged amino acid to the charged amino acid that time net charge on the system becomes non-zero. To keep the net charge of the system constrained to zero, I want to mutate water molecules to Na or Cl ions with protein amino acid mutation.

I want to know, how can i make a dual topology file for water ion transformation and use it in Gromacs.

Can you please help me with this?