# Refinement of the models from haddock2.2 webserver

**URL:** <https://ask.bioexcel.eu/t/refinement-of-the-models-from-haddock2-2-webserver/1028>\
**Category:** HADDOCK\
**Created:** [June 23, 2018, 11:07am UTC](https://ask.bioexcel.eu/t/refinement-of-the-models-from-haddock2-2-webserver/1028 "2018-06-23T11:07:23Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\
**Post date:** [June 23, 2018, 11:07am UTC](https://ask.bioexcel.eu/t/refinement-of-the-models-from-haddock2-2-webserver/1028/1 "2018-06-23T11:07:23Z")

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Dear all,

As the models generated from haddock2.2 webserver only contain the protons bonded to a polar atom, I want to refine these models in water plus the NOE constraints ( the input structures for docking calculated by NMR).

Is there a way only to do the water refinement by using the local installation haddock2.2?

Thanks.

Best  
Changdong

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**Author:** ![joaor](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaor/32/194_2.png) [@joaor](https://ask.bioexcel.eu/u/joaor)\
**Post date:** [June 23, 2018, 6:41pm UTC](https://ask.bioexcel.eu/t/refinement-of-the-models-from-haddock2-2-webserver/1028/2 "2018-06-23T18:41:43Z")

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There is an option in the ‘Expert Interface’ to keep all hydrogens in the molecule, under the ‘Distance Restraints’ tab. Ask for a higher access level and you will be able to use NOE restraints during the refinement.

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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 24, 2018, 5:14pm UTC](https://ask.bioexcel.eu/t/refinement-of-the-models-from-haddock2-2-webserver/1028/3 "2018-06-24T17:14:39Z")

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And to mimic the refinement interface settings, while keeping all hydrogens as explained above by Joao follow the recipe given on the HADDOCK manual pages at:

[http://www.bonvinlab.org/software/haddock2.2/tips/advanced\_refinement/](http://www.bonvinlab.org/software/haddock2.2/tips/advanced_refinement/)

You need for that to use (and have access) to the guru interface

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**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\
**Post date:** [June 27, 2018, 3:20am UTC](https://ask.bioexcel.eu/t/refinement-of-the-models-from-haddock2-2-webserver/1028/4 "2018-06-27T03:20:00Z")

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Dear Dr.Alexandre Bonvin and Joao Rodrigues,

That works, thanks.

Best