# Refinement with HADDOCK

**URL:** <https://ask.bioexcel.eu/t/refinement-with-haddock/2663>\
**Category:** HADDOCK\
**Created:** [November 26, 2020, 4:00pm UTC](https://ask.bioexcel.eu/t/refinement-with-haddock/2663 "2020-11-26T16:00:39Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mieczyslaw](https://avatars.discourse-cdn.com/v4/letter/m/aeb1de/32.png) [@mieczyslaw](https://ask.bioexcel.eu/u/mieczyslaw)\
**Post date:** [November 26, 2020, 4:00pm UTC](https://ask.bioexcel.eu/t/refinement-with-haddock/2663/1 "2020-11-26T16:00:39Z")

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HADDOCK final step is MD refinement in water.

1. How can I find the MD parameters HADDOCK used?
2. Can I only run this stage on a protein complex with small ligands instead of full docking, simply to optimize the final geometry (bonds, angles), maybe remove some clashes and adjust sidechains?

Thanks.

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [November 26, 2020, 5:16pm UTC](https://ask.bioexcel.eu/t/refinement-with-haddock/2663/2 "2020-11-26T17:16:27Z")

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You can find more information about the MD parameters in the [Docking Protocol](https://www.bonvinlab.org/software/haddock2.4/run/#docking-protocol) section.

Our webserver has a dedicated [Refinement Interface](https://wenmr.science.uu.nl/haddock2.4/refinement/1), you could achieve the same on the local setup using the same parameters: [https://wenmr.science.uu.nl/haddock2.4/settings#refinement](https://wenmr.science.uu.nl/haddock2.4/settings#refinement)!