# Protein+one ligand+cofactor

**URL:** <https://gromacs.bioexcel.eu/t/protein-one-ligand-cofactor/2647>\
**Category:** User discussions\
**Tags:** forcefield, mdrun\
**Created:** [August 5, 2021, 8:10pm UTC](https://gromacs.bioexcel.eu/t/protein-one-ligand-cofactor/2647 "2021-08-05T20:10:00Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![fareedasaad](https://avatars.discourse-cdn.com/v4/letter/f/7feea3/32.png) [@fareedasaad](https://gromacs.bioexcel.eu/u/fareedasaad)\
**Post date:** [August 5, 2021, 8:10pm UTC](https://gromacs.bioexcel.eu/t/protein-one-ligand-cofactor/2647/1 "2021-08-05T20:10:00Z")

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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

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**Author:** ![bgrokm](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/bgrokm/32/1027_2.png) [@bgrokm](https://gromacs.bioexcel.eu/u/bgrokm)\
**Post date:** [August 31, 2021, 3:37pm UTC](https://gromacs.bioexcel.eu/t/protein-one-ligand-cofactor/2647/2 "2021-08-31T15:37:57Z")

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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](https://angeloraymondrossi.github.io/workshop/charmm-gromacs-small-organic-molecules-new.html)

- [Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS — Bioinformatics Review](https://bioinformaticsreview.com/20200712/tutorial-md-simulation-of-a-protein-ligand-complex-using-gromacs/)