Error submitting a trimmer structure for docking


Im doing protein-protein docking and after submitting my trimmer on the haddock server, i get this message saying:

There was an inconsistency in your data

Error message

First pdb file contains multiple chains with overlapping numbering: P1 - B1

What can i do if i already rename every segment and chain of my trimmer to prevent the “overlapping”, or in which part im failing? By the way, its a homo-trimmer protein.

Thanks, by the way.

Protein modified after completing the docking process


Renaming chains is not enough to get rid of overlapping residue IDs, you should make sure that not residue number is identical among all the chains of a molecule you want to dock. The numbering should be continuous between the different chains and, for instance, if you have residue from 1 to 100 in chain A, residue number in chain B should start at 101 and so on.

Good luck with your docking run,




Thanks for the answer, i renumbered all the structure from beginning to final, with correlatives numbers and get fix it.


PS: This forum is searchable :slight_smile: Look for homodimers for example. Plenty of tips how to do this simply using our pdb-tools scripts