Protein ligand docking at low pH

HADDOCK
1

Hi, I am a new user of Haddock. My purpose is to perform protein-ligand docking. We took the structure of protein from constant ph molecular dynamics (using Amber) at pH 2 after clustering. Next, we try to dock representative pdb structure obtained from clustering with oleic acid. My question is, during docking using HADDOCK whether protonation state of titrable residues of representative protein structure will change or remain fixed. As for my system I need to fix the protonation state during docking. Thanks in advance. Any kind of help will be appreciated.

Best Regards
Abhik
S N Bose National Centre for Basic Sciences
India

2

You would have to change the naming of ASP and GLU residues in your PDB file to indicate they are protonated.

ASP → ASH
GLU → GLH

And you can manually set the protonation state of Histidine at submission time (requires guru access)