# Ligand structure changes after docking

**URL:** <https://ask.bioexcel.eu/t/ligand-structure-changes-after-docking/1748>\
**Category:** HADDOCK\
**Created:** [November 9, 2019, 9:45pm UTC](https://ask.bioexcel.eu/t/ligand-structure-changes-after-docking/1748 "2019-11-09T21:45:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Sahar](https://avatars.discourse-cdn.com/v4/letter/s/ea5d25/32.png) [@Sahar](https://ask.bioexcel.eu/u/Sahar)\
**Post date:** [November 9, 2019, 9:45pm UTC](https://ask.bioexcel.eu/t/ligand-structure-changes-after-docking/1748/1 "2019-11-09T21:45:23Z")

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Hi everyone,  
I am using HADDOCK 2.2 and 2.4 for RNA\_ligand docking. I have a problem about changes in my ligand after docking. I prepared my ligand in two different ways (MOE\_Wash and geometric optimization using GAMESS). However, after the docking I found that I am getting a different protonation state of the ligand (some bonds will change from double to single and a resonance appear in the system). I also used PRODRG for making the input file of the ligand, by only keeping the polar hydrogens, however I am still getting the same results. Does anyone experienced the same problem and a possible solution?

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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 10, 2019, 9:35am UTC](https://ask.bioexcel.eu/t/ligand-structure-changes-after-docking/1748/2 "2019-11-10T09:35:23Z")

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You don’t have control on this on the server.  
The only solution would be to run a local version of HADDOCK and provide the required ligand topology and parameter files in CNS format.

Software like acpype can be useful for this. E.g.:

[https://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder](https://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder)