# Protein modified after completing the docking process **URL:** \ **Category:** HADDOCK\ **Created:** [September 30, 2018, 3:54pm UTC](https://ask.bioexcel.eu/t/protein-modified-after-completing-the-docking-process/1203 "2018-09-30T15:54:55Z")\ **Posts on this page:** 1\ **Showing post:** 2
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [October 3, 2018, 10:51am UTC](https://ask.bioexcel.eu/t/protein-modified-after-completing-the-docking-process/1203/2 "2018-10-03T10:51:47Z")
Did you renumber your trimer to avoid overlap in numbering? Check the forum for tips on how to handle homomers, e.g.: > [@Setup for protein dock to protein homodimer](http://ask.bioexcel.eu/t/setup-for-protein-dock-to-protein-homodimer/849): > > The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2) Hello, Does anybody know how to setup protein to dock a protein homodimer. Since there are two chains in a homodimer (A subunit and B subunit), how can I assign the residues in A subunit and/or in B subunit. What is the format I should use. Please let me know. Thank you, Han > [@Error submitting a trimmer structure for docking](http://ask.bioexcel.eu/t/error-submitting-a-trimmer-structure-for-docking/1173): > > 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. But looking at your exploded models, I suspect your starting models are not of very good quality and must have clashes… --- _[View the full topic](https://ask.bioexcel.eu/t/protein-modified-after-completing-the-docking-process/1203)._