# Distorted output structures

**URL:** <https://ask.bioexcel.eu/t/distorted-output-structures/3785>\
**Category:** HADDOCK\
**Created:** [June 27, 2022, 11:17am UTC](https://ask.bioexcel.eu/t/distorted-output-structures/3785 "2022-06-27T11:17:00Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![gabrielep](https://avatars.discourse-cdn.com/v4/letter/g/ec9cab/32.png) [@gabrielep](https://ask.bioexcel.eu/u/gabrielep)\
**Post date:** [June 27, 2022, 11:17am UTC](https://ask.bioexcel.eu/t/distorted-output-structures/3785/1 "2022-06-27T11:17:00Z")

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Hello,

I’ve installed local version of haddock2.4 and I’m trying to dock large multi-chain complexes (\>10 chains).

I followed the protein-protein docking tutorial and, on top of that, I only modified the run.cns file turning on the center of mass restraints and increasing the sampling as it is stated in this post:

> [@Protein Protein docking without restraint definitions](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545):
>
> Hi Prof. Bonvin, I have experienced with bound ligand protein-protein docking with restraint definition with 5A active site residue from the ligand. HADDOCK generated almost similar poses as reference. Now, assume if I don’t have information about ligand in the second protein. I don’t know the second protein where exactly bind with the first protein. Blindly, I would like to submit a job. Is it possible to submit a job without defining active and passive residues in HADDOCK interface? If yes th…

Runs seems to complete successfully but in the ave.pdb results I find completely distorted structures. I also tried using just 2 chains, and the amount of distortion seems lower but still the structures are completely destroyed.

 ![image1](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/fc7f85a32afbde95d2e209126f75b3d9e9d8a7fe.png)

Do you have any idea of why this is happening?

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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:** [July 6, 2022, 4:17pm UTC](https://ask.bioexcel.eu/t/distorted-output-structures/3785/2 "2022-07-06T16:17:05Z")

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The average file has no meaning…especially not if many different models are generated. Look at the individual models.

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**Author:** ![gabrielep](https://avatars.discourse-cdn.com/v4/letter/g/ec9cab/32.png) [@gabrielep](https://ask.bioexcel.eu/u/gabrielep)\
**Post date:** [July 6, 2022, 5:23pm UTC](https://ask.bioexcel.eu/t/distorted-output-structures/3785/3 "2022-07-06T17:23:55Z")

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Oh that was quite simple.  
I got tricked checking an avg.pdb file from a sample run you provided somewhere, which actually contains a good structure.

Sorry for the silly question and thanks for your answer 🙂