Another doubt about covalent bound ligands

GROMACS version: 2021
GROMACS modification: No

Dear users,

I read the other topics here about covalent ligands and other tutorials… but there are some details I didn’t understand. Could you please help me?

I’m working with a cysteine protease and some ligands covalently bound to the cysteine residue. This protein is a dimer and I have the ligand coupled to both active sites.

I obtained the .PDB file, created mol2 file for the ligand (closing the valence with a hydrogen atom), got the .STR file through CGenFF and the .ITP/PRM files from it. After that, I opened the aminoacids.RTP, copied the [DCYS] [atoms], [bonds], [impropers], [cmap] and pasted below, changing [DCYS] to [NCYS] and adding the [atoms] and [bonds] from the ligand.ITP file (deleting the hydrogen atom/bond inserted to close the valence).

My first question is: Is there anything wrong until now or are the steps right?

Second: Should I delete the ligands in the PDB file and add them as part of the CYS residues (changing the name of the residue for NCYS) before creating the topology (pdb2gmx)?

Thank you for your help,
Xavier