# Incorrect docking results

**URL:** <https://ask.bioexcel.eu/t/incorrect-docking-results/4244>\
**Category:** HADDOCK\
**Created:** [April 3, 2023, 2:05pm UTC](https://ask.bioexcel.eu/t/incorrect-docking-results/4244 "2023-04-03T14:05:33Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\
**Post date:** [April 3, 2023, 2:05pm UTC](https://ask.bioexcel.eu/t/incorrect-docking-results/4244/1 "2023-04-03T14:05:33Z")

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Hi  
I am trying to dock an protein and peptide. When I had the basic version I docked without restraints (only active/passive) and it worked.  
but when I was upgraded to GURU and used restraints, the docking score became -1.2 and in the PDB file I see them very far apart.  
What can cause this?  
project ID 226078  
Thx!

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<div class="post-metadata">

**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:** [April 3, 2023, 4:56pm UTC](https://ask.bioexcel.eu/t/incorrect-docking-results/4244/2 "2023-04-03T16:56:10Z")

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Wrong restraints?

How did you create those? Did you specify the correct chainIDs?

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<div class="post-metadata">

**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\
**Post date:** [April 3, 2023, 9:14pm UTC](https://ask.bioexcel.eu/t/incorrect-docking-results/4244/3 "2023-04-03T21:14:40Z")

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I found them using NOESY spectrum,  
example for a restraint I used is  
assign(segid A and resid 24 and name HD)(segid B and resid 3 and name HG\*) 3.5 2.0 2.5  
and I used the correct chain ID, any ideas?  
thx!

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<div class="post-metadata">

**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:** [April 4, 2023, 5:04am UTC](https://ask.bioexcel.eu/t/incorrect-docking-results/4244/4 "2023-04-04T05:04:17Z")

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By default all non polar hydrogens are deleted… 🙂

You can turn off that option in the distance restraint menu

And make sure the naming of your protons in that case correspond to the naming used by HADDOCK.