# Protein-ligand + ligand docking?
**URL:** https://ask.bioexcel.eu/t/protein-ligand-ligand-docking/3778
**Category:** HADDOCK
**Created:** [June 21, 2022, 7:42pm UTC](https://ask.bioexcel.eu/t/protein-ligand-ligand-docking/3778 "2022-06-21T19:42:30Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@hughhig](https://ask.bioexcel.eu/u/hughhig)
#### Post date: [June 21, 2022, 7:42pm UTC](https://ask.bioexcel.eu/t/protein-ligand-ligand-docking/3778/1 "2022-06-21T19:42:30Z")
Hello,
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?
Best,
Hugh
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [June 22, 2022, 6:49pm UTC](https://ask.bioexcel.eu/t/protein-ligand-ligand-docking/3778/2 "2022-06-22T18:49:51Z")
Simply keep your lipid in the structure you give to HADDOCK.
Do define it as HETATM