I put "add_h_edit.inp" in my home directory on apollo. YOu will need to be modified the input for residues other than lys or arg, but it should not be difficult. It can be used after you use mutate.pl. Once you get XXX.pdb use the input directly to "fix" ( look for IC edit statements this is where you change resnumber and type and the desired dihedrals ) the mutated side chain orientation. Good Luck!