# Using ensemble pdb not working on web server

**URL:** <https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794>\
**Category:** HADDOCK\
**Created:** [January 10, 2020, 5:13pm UTC](https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794 "2020-01-10T17:13:05Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![mahtab](https://avatars.discourse-cdn.com/v4/letter/m/898d66/32.png) [@mahtab](https://ask.bioexcel.eu/u/mahtab)\
**Post date:** [January 10, 2020, 5:13pm UTC](https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794/1 "2020-01-10T17:13:05Z")

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Hi,  
I am trying to dock a protein-DNA complex using a single model for the protein and an ensemble of 20 models for the DNA on the haddock web server. If we split the DNA ensemble up with (pdb\_splitmodel.py) and submit a single structure, haddock works. If we submit the original or reassembled (pdb\_mkensemble.py) ensemble haddock fails. The log for the latter can be found at [http://milou.science.uu.nl/serviceresults/HADDOCK2.2/2525349827/010920\_dsDNA\_20c/](http://milou.science.uu.nl/serviceresults/HADDOCK2.2/2525349827/010920_dsDNA_20c/)  
We have made sure that the pdbs are in the correct format using pdb\_validate.py/pdb\_chkensemble.py.  
Any help would be greatly appreciated.  
Thanks,  
Mahtab

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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:** [January 11, 2020, 3:11pm UTC](https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794/2 "2020-01-11T15:11:05Z")

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Something is wrong with your ensemble. All submitted models are empty files.

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<div class="post-metadata">

**Author:** ![mahtab](https://avatars.discourse-cdn.com/v4/letter/m/898d66/32.png) [@mahtab](https://ask.bioexcel.eu/u/mahtab)\
**Post date:** [January 14, 2020, 6:17pm UTC](https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794/3 "2020-01-14T18:17:02Z")

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Hi,  
Thanks to your response.  
I checked my pdb again and it was not empty.  
I submitted the same pdb again and it failed again ( [https://milou.science.uu.nl/serviceresults/HADDOCK2.2/2525349827/011420/](https://milou.science.uu.nl/serviceresults/HADDOCK2.2/2525349827/011420/))  
This is the link to the pdb file I used.([https://www.dropbox.com/s/pcwrqg29xfrf7qu/dsDNA\_20c.pdb?dl=0](https://www.dropbox.com/s/pcwrqg29xfrf7qu/dsDNA_20c.pdb?dl=0))

Thanks for your help,  
Mahtab

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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:** [January 15, 2020, 8:39am UTC](https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794/4 "2020-01-15T08:39:51Z")

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Hi Mahtab

You are right! There was a problem on the server side, but it only happened for large systems, with an ensemble of models…  
Should be fine now.

```
https://milou.science.uu.nl/serviceresults/HADDOCK2.2/1111111111/test-dna6/

```

And I noticed your defined your DNA as protein-DNA while it is only DNA.  
The type of molecule applies to each molecule separately and not to the complex.

Cheers  
Alexandre

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<div class="post-metadata">

**Author:** ![mahtab](https://avatars.discourse-cdn.com/v4/letter/m/898d66/32.png) [@mahtab](https://ask.bioexcel.eu/u/mahtab)\
**Post date:** [January 27, 2020, 10:58pm UTC](https://ask.bioexcel.eu/t/using-ensemble-pdb-not-working-on-web-server/1794/5 "2020-01-27T22:58:48Z")

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Thank you very much

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