# Desolvation-energy

**URL:** <https://ask.bioexcel.eu/t/desolvation-energy/5941>\
**Category:** HADDOCK\
**Created:** [November 9, 2025, 8:00am UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941 "2025-11-09T08:00:28Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\
**Post date:** [November 9, 2025, 8:00am UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941/1 "2025-11-09T08:00:28Z")

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The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [HADDOCK – Bonvin Lab](http://www.bonvinlab.org/software/haddock2.4)

Hi, I recently run a protein ligand docking in haddock 2.4 webserver. The result gave me a positive desolvation energy. Is it something to worry about? Like should I change something in the parameters while running the docking. I am trying to reproduce a published result and they have reported a negative desolvation energy. I am uploading the screenshot of result for reference.

Thank you,

Vibes

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/b/b4b877864e597893e2a33c228b5d23ab40a43510.png)

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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 9, 2025, 10:17am UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941/2 "2025-11-09T10:17:58Z")

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Nothing to worry about - it happens.

And for small ligands it might not tell that much anyway.

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**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\
**Post date:** [November 9, 2025, 10:42am UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941/3 "2025-11-09T10:42:52Z")

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Thank you for your reply. I am new to docking…could you please tell me what all parameters among the above given by haddock should I focus on to say that this ligand has docked well to the protein?

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [November 10, 2025, 8:03am UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941/4 "2025-11-10T08:03:50Z")

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The only way for you to know if the ‘ligand has docked well’, is to compare it with a reference structure, and compute the ligand-RMSD.  
If you obtain the same conformation (ligand-RMSD as small as possible), you can say you managed to reproduce the result of that particular paper.

Also, note that reported values here are per-cluster (1.8 +/- 0.5 in that case).  
If you download the corresponding structures, you can investigate the actual scores in the PDB file for each complex, and maybe one of them contains a negative desolvation energy.

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**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\
**Post date:** [November 10, 2025, 10:01pm UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941/5 "2025-11-10T22:01:54Z")

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Thank you very much