We now have a solvated system that contains a charged protein. The output of pdb2gmx told us that the protein has a net charge of +6e (based on its amino acid composition). If you missed this information in the pdb2gmx output, look at the last line of your [ atoms ] directive in topol.top; it should read (in part) "qtot 6." Since life does not exist at a net charge, we must add ions to our system.

Use grompp to assemble a .tpr file, using any .mdp file. I use an .mdp file for running energy minimization, since they require the fewest parameters and are thus the easiest to maintain. For example, this one.

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

We now pass our .tpr file to genion:

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral

The names of the ions specified with -pname and -nname were force field-specific in previous versions of GROMACS, but were standardized in version 4.5. The specified atom names are always the elemental symbol in all capital letters, along with the [ moleculetype ]. Residue names may or may not append the sign of the charge (+/-). Refer to ions.itp for proper nomenclature if you encounter difficulties.

Your [ molecules ] directive should now look like:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
JZ4                 1
SOL             10228
CL                  6