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.
Cheers
Dear VGPReys,
It is indeed the second option
The ligand I am using is GPP with hetatoms, not a peptide, nor a protein.
Thank you for your reply!
Best,
Joel