# Need to dock 1000 peptide for one protein in HPC. Is there is any way to do that in one job?

**URL:** <https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959>\
**Category:** Uncategorized\
**Created:** [November 25, 2025, 9:33pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959 "2025-11-25T21:33:22Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\
**Post date:** [November 25, 2025, 9:33pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959/1 "2025-11-25T21:33:22Z")

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Hello,

I want to dock 1000 peptide against one protein. Is that any efficient way to do that other than one json for each. Also, I have to use HPC installation for this. Can I generate the output in the same format as that of web server?

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:** [November 26, 2025, 7:53am UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959/2 "2025-11-26T07:53:41Z")

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The new HADDOCK3 version does generate similar reports as the web server.

> **[HADDOCK3](https://www.bonvinlab.org/software/haddock3/)**

And to run a large number of docking runs, you can use for example the haddock-runner

> **[GitHub - haddocking/haddock-runner: Run large scale HADDOCK simulations using multiple...](https://github.com/haddocking/haddock-runner)**
>
> Run large scale HADDOCK simulations using multiple input molecules in different scenarios

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<div class="post-metadata">

**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\
**Post date:** [November 26, 2025, 2:19pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959/3 "2025-11-26T14:19:56Z")

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That’s great. Ill reconfigure my system and also will try the haddock runner.

Thank you so much for your prompt response.

Regards

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**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\
**Post date:** [December 5, 2025, 4:33pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959/4 "2025-12-05T16:33:40Z")

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Hello Bovin,

I am unable to find any tutorial for haddock3+haddock-runner.

How to use both these together.

Regards

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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:** [December 5, 2025, 8:42pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959/5 "2025-12-05T20:42:21Z")

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Check [https://www.bonvinlab.org/haddock-runner/](https://www.bonvinlab.org/haddock-runner/)

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**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\
**Post date:** [December 8, 2025, 9:06pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959/6 "2025-12-08T21:06:29Z")

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Thank you so much. Ill check.