I follow the protein-ligand simulation tutorial protocol. For my own protein-ligand simulation, I give the following commands at the ion addition stage:

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

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