# Covalent Protein-Ligand complex simulation

**URL:** <https://gromacs.bioexcel.eu/t/covalent-protein-ligand-complex-simulation/9707>\
**Category:** User discussions\
**Tags:** forcefield, mdp-parameters, simulation-setup\
**Created:** [July 22, 2024, 4:17pm UTC](https://gromacs.bioexcel.eu/t/covalent-protein-ligand-complex-simulation/9707 "2024-07-22T16:17:50Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![rafaeljctravassos](https://avatars.discourse-cdn.com/v4/letter/r/da6949/32.png) [@rafaeljctravassos](https://gromacs.bioexcel.eu/u/rafaeljctravassos)\
**Post date:** [July 22, 2024, 4:17pm UTC](https://gromacs.bioexcel.eu/t/covalent-protein-ligand-complex-simulation/9707/1 "2024-07-22T16:17:50Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hello,

I’ve started studying molecular dynamics where I have a transmembrane protein that I want to be covalently bond to a ligand (MC-Val-Cit-Doxorubicin). I performed docking between the ligand to the protein and built a bond between them ( C2 maleimide of the ligand binds to the cysteine, CYS150, of the protein). Forward, I built the system in CHARMM-GUI and extracted the files that will serve as input for gromacs. However, in CHARMM I lose the covalent bond of the ligand to the protein, because there is a ‘Bond order error’. How can I get around this problem?

Regards,  
Rafael