# Cannot select both chains of MHC II complex for docking

**URL:** <https://ask.bioexcel.eu/t/cannot-select-both-chains-of-mhc-ii-complex-for-docking/5558>\
**Category:** HADDOCK\
**Tags:** haddock, support, community\
**Created:** [April 2, 2025, 5:08am UTC](https://ask.bioexcel.eu/t/cannot-select-both-chains-of-mhc-ii-complex-for-docking/5558 "2025-04-02T05:08:30Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sauda07](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@sauda07](https://ask.bioexcel.eu/u/sauda07)\
**Post date:** [April 2, 2025, 5:08am UTC](https://ask.bioexcel.eu/t/cannot-select-both-chains-of-mhc-ii-complex-for-docking/5558/1 "2025-04-02T05:08:30Z")

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Hello,  
I want to dock peptide with mhcii complex with both chains, ie. A and B but after uploading the pdb file in haddock webserver, How do I involve both chains for docking? Thanks!!

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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:** [April 2, 2025, 7:19am UTC](https://ask.bioexcel.eu/t/cannot-select-both-chains-of-mhc-ii-complex-for-docking/5558/2 "2025-04-02T07:19:09Z")

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Each molecule must consist of a unique chain.

I.e. you might have to combine your A and B chains into one single chain with non-overlapping residue numbering

The forum is searchable and this question has been answered multiple times 🙂