Error in running HADDOCK

Hi there,

I am getting the following error while trying to do protein-protein docking:

There was an inconsistency in your data

Error message
Instances of ligand 604 do not contain the same atoms
Directory of the run:

Since only one of the protein contained the residue #604, I checked and it seemed fine. So could someone kindly point me to the error reason?



Hello Arjun,

Looking at your 1st PDB file, it appears that you have 2 ligands named “604” with residue IDs 1 and 2. And these two ligands have different atoms since the 1st ligand lacks atoms C1, C2 and C3.

I hope this will help you,


Dear Mikael,

Thank you so much! I have deleted the ligand and now it works! Sorry for my stupidity.