# Docking two inhibitor bound proteins

**URL:** https://ask.bioexcel.eu/t/docking-two-inhibitor-bound-proteins/3039
**Category:** HADDOCK
**Created:** [June 3, 2021, 12:06pm UTC](https://ask.bioexcel.eu/t/docking-two-inhibitor-bound-proteins/3039 "2021-06-03T12:06:51Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![emartis12](https://avatars.discourse-cdn.com/v4/letter/e/439d5e/32.png) [@emartis12](https://ask.bioexcel.eu/u/emartis12)
#### Post date: [June 3, 2021, 12:06pm UTC](https://ask.bioexcel.eu/t/docking-two-inhibitor-bound-proteins/3039/1 "2021-06-03T12:06:51Z")

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Hello @amjjbonvin

I want to dock two proteins that are bound to their respective inhibitors.

I understand how to edit the ligand.param and ligand.top files in toppar directory for one ligand, however, I am unable to understand how to deal when I have two ligands.

Any suggestions would be a great help.

Regards  
@emartis12

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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: [June 3, 2021, 12:19pm UTC](https://ask.bioexcel.eu/t/docking-two-inhibitor-bound-proteins/3039/2 "2021-06-03T12:19:06Z")

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Running locally I assume?

You should then combine the two topo/param files into one, make sure there is no overlap in the atom types naming.

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<div class="post-metadata">

### Author: ![emartis12](https://avatars.discourse-cdn.com/v4/letter/e/439d5e/32.png) [@emartis12](https://ask.bioexcel.eu/u/emartis12)
#### Post date: [June 3, 2021, 12:41pm UTC](https://ask.bioexcel.eu/t/docking-two-inhibitor-bound-proteins/3039/3 "2021-06-03T12:41:35Z")

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Yes, running locally.

Thanks a ton for the suggestion.

Best regards  
@emartis12