Protein+one ligand+cofactor

[fareedasaad]

GROMACS version:5.1
GROMACS modification: No
Greetings
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 topol.top 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

[bgrokm]

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:

• GROMACS: MD Simulation of a Protein-Ligand Complex

• Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS — Bioinformatics Review