genion

The genion program reads a run input (.tpr) file and adds ions to the system.

A common problem that new users make is specifying the wrong ion names (or leaving the defaults in place).  You must use the -pname and -nname flags to specify the molecule names of the ions as they appear in ions.itp for your chosen force field.  Do not mistakenly use the atom name, or residue name, or make something random up.

As of GROMACS version 4.5, all  molecule, atom, and residue names for ions have been standardized.  Atom types are still force field-dependent.  For example, in GROMOS force fields the atom type for chloride is CL-, but the molecule, residue, and atom names are CL.  Exceptions do exist for some ion types, so be sure you are familiar with the expectations of your force field.  If you do not properly name the ions by their molecule names when running genion, grompp will complain later.  For example, this error message often arises.