Ligand are residues not shown

Hi there,

Since I do not know the active sites of my protein, I am following this ab initio tutorial: HADDOCK2.4 small molecule binding site screening – Bonvin Lab

Haddock 2.4 does run; however, the ligand that has 39 residues only shows 1 (as in attached image).

How can I solve this problem please?

Dear Joel,

Thanks for your interest in using haddock for your research.

Are you sure your ligand has 39 resiudes ?

  • If it is the case, then maybe consider it as a peptide or a protein
  • If you ligand has 39 atoms, then everything is fine. Indeed, haddock is attributing the residue name LIG to ligands in the PDB file, therefore resulting in a single residue representation. Hence, showing number of residues = 1 is perfectly fine.

With the hope that this answer help you.


Dear VGPReys,

It is indeed the second option :slight_smile: The ligand I am using is GPP with hetatoms, not a peptide, nor a protein.

Thank you for your reply!