# PH setting in haddock

**URL:** <https://ask.bioexcel.eu/t/ph-setting-in-haddock/519>\
**Category:** HADDOCK\
**Created:** [October 4, 2017, 11:26am UTC](https://ask.bioexcel.eu/t/ph-setting-in-haddock/519 "2017-10-04T11:26:37Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![HosseinLanjanian](https://avatars.discourse-cdn.com/v4/letter/h/dec6dc/32.png) [@HosseinLanjanian](https://ask.bioexcel.eu/u/HosseinLanjanian)\
**Post date:** [October 4, 2017, 11:26am UTC](https://ask.bioexcel.eu/t/ph-setting-in-haddock/519/1 "2017-10-04T11:26:37Z")

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Hi  
I would like to study the aggregation of a protein in the different PHs.  
To this aim I run MD simulatiopn in Gromacs and set the protenition state regarding to the desired PH.  
Then I used the final frame of the Gromacs output as the in put of the Haddock AND docked this pdb with itself.  
But the results are not confirmed by the experiments. I think it need to add H+ in the invironment.  
Is it possible that we add a spesific concenteration of the H+ to the solvetion IN haddock?

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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:** [October 4, 2017, 4:03pm UTC](https://ask.bioexcel.eu/t/ph-setting-in-haddock/519/2 "2017-10-04T16:03:43Z")

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The simple answer is no…

The only control you can have is about the protonation state of Histidines.