# Protein-protein docking parameters

**URL:** <https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776>\
**Category:** HADDOCK\
**Tags:** gromacs, biobb, haddock, support, tutorials\
**Created:** [June 30, 2025, 11:57pm UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776 "2025-06-30T23:57:16Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\
**Post date:** [June 30, 2025, 11:57pm UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776/1 "2025-06-30T23:57:16Z")

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Hello  
I would like to perform protein-protein docking, and I do not have any experimental data showing how they are interacting and what is the binding interface of them. But, I used PesTo webserver and other online tools to identify the active residues for input in HADDOCK docking webserver. Now, I am in the 3rd step (Docking parameters). I just have a couple of questions. Do you recommend applying any restraints for my system (such as center-of-mass? I do not know which parameters should be True and marked for my aim?  
Please guide me though that.

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [July 1, 2025, 9:42am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776/2 "2025-07-01T09:42:58Z")

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Dear Negin,

If you used PesTo to identify potential interacting residues, you should define them as `active` in the 2nd step, for each molecule, and make the automatic definition of neighbor residues as `passive`. Then in the 3rd step, forget about center-of-mass restraints, as the ones detected by PesTo (the active ones) will be used to drive the docking.

Cheers

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**Author:** ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko)\
**Post date:** [July 1, 2025, 9:48am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776/3 "2025-07-01T09:48:29Z")

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And I’d suggest leaving another docking parameters as default. Since you’re dealing with protein-protein docking, default values should be suitable for this task