# Running a protein-ligand simulation with covalent bonds

**URL:** <https://gromacs.bioexcel.eu/t/running-a-protein-ligand-simulation-with-covalent-bonds/4473>\
**Category:** User discussions\
**Created:** [July 17, 2022, 8:10am UTC](https://gromacs.bioexcel.eu/t/running-a-protein-ligand-simulation-with-covalent-bonds/4473 "2022-07-17T08:10:59Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Bidisha](https://avatars.discourse-cdn.com/v4/letter/b/df705f/32.png) [@Bidisha](https://gromacs.bioexcel.eu/u/Bidisha)\
**Post date:** [July 17, 2022, 8:10am UTC](https://gromacs.bioexcel.eu/t/running-a-protein-ligand-simulation-with-covalent-bonds/4473/1 "2022-07-17T08:10:59Z")

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GROMACS version: 2018  
Hello everyone,  
I am new to GROMACS. I am trying to run a simulation of a protein with chromophore FMN attached covalently with the protein using Amber ff99sb forcefield. If I strip away the ligand from the protein while generating the topology files then the covalent bond is breaking. How should I define the covalent bond to the system? What should I do? How should I proceed? Thank you very much for your help.