# Setup for protein dock to protein homodimer

**URL:** <https://ask.bioexcel.eu/t/setup-for-protein-dock-to-protein-homodimer/849>\
**Category:** HADDOCK\
**Created:** [March 19, 2018, 6:13pm UTC](https://ask.bioexcel.eu/t/setup-for-protein-dock-to-protein-homodimer/849 "2018-03-19T18:13:45Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Han\_Feng](https://avatars.discourse-cdn.com/v4/letter/h/c2a13f/32.png) [@Han\_Feng](https://ask.bioexcel.eu/u/Han_Feng)\
**Post date:** [March 19, 2018, 6:13pm UTC](https://ask.bioexcel.eu/t/setup-for-protein-dock-to-protein-homodimer/849/1 "2018-03-19T18:13:45Z")

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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

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**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:** [March 20, 2018, 12:36am UTC](https://ask.bioexcel.eu/t/setup-for-protein-dock-to-protein-homodimer/849/2 "2018-03-20T00:36:40Z")

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Hi Han

There are quite a few answers already to that question in our forum (which is by the way searchable). E.g.:

> [@Dealing with dimers](http://ask.bioexcel.eu/t/dealing-with-dimers/42):
>
> Hellow everybody I have problems using Haddock for dimers. I’ve received several different messages: Using pdb (from pdb databse) There was an inconsistency in your data Error message First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble using a pdb with only one chain (but is a dimer) There was an inconsistency in your data Error message First pdb file contai…

In short you need to renumber the second monomer to avoid overlap in residue number and give it to HADDOCK as a single chain PDB.