I am doing docking between two proteins. Let's say protein A and protein B. Protein B has a modified amino acid composed of serine, phosphopantetheine, and a long acyl part. Before docking, I generated parameter file (.params) for the modified amino acid by molfile_to_params.py with -a flag. I also generated conformers for this modified amino acid (if we take it as a ligand). Now, I was wondering whether I should do protein-protein or protein-ligand docking. Does it make sense to first do protein-protein docking and then protein-ligand docking?
It is noteworthy to mention that I just did protein-protein docking and the output structures are not much different from each other (standard deviation close to zero) and even from the input structure.
Any suggestion is appreciated.