Protein+one ligand+cofactor

GROMACS version:5.1
GROMACS modification: No
I’m learning how to simulate a system made of protein, ligand, and a cofactor, I don’t know how to make the program differentiate between the cofactor and the Ligand. in which way should I prepare the the .itp files and .prm so that it will work, I keep on getting errors. I performed the tutorial successfully but the case in my project is different

It may be helpful to use a more recent version of GROMACS since some of the file conventions have changed. Have you tried any of the following: