Protein-ligand + ligand docking?


I’m working with a membrane-bound enzyme that has two types of substrate, a small-molecule and a lipid. From collaborators we have a structure from a fuller simulation of the protein and lipid, but some initial attempts to get the small-molecule ligand position with Haddock have been running into trouble where it ends up in what is known to be the lipid’s binding site. Since the web server lists a type of molecule to dock as ‘protein or protein-ligand’, is there a way to try docking the small molecule (ligand2) to the combined structure of the lipid and enzyme (protein-ligand1), or do I need to try incorporating this information less directly, e.g. by manually excluding the ligand1 binding site in the list of passive residues?


Simply keep your lipid in the structure you give to HADDOCK.
Do define it as HETATM