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.


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

Hi, sorry for asking… how did you renumbering the residues? because its also happened to me, the protein overlapping numbering… if you don’t mind, can you explain the protocol how to do that? sorry i am still new one… or you can email me at

The forum is searchable and the answer has been given several times…

Search for example for dimer, renumbering …

Thank you Prof… and I also would like to try DisVis server, and may I know how can I get the restraint file? Or I need to run the job from cross-link restraint at first?

Thank you in advance.

Check our online tutorial about the disvis server at