Running a protein-ligand simulation with covalent bonds

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.