Using ensemble pdb not working on web server

HADDOCK
1

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/
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

2

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

3

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/)
This is the link to the pdb file I used.(https://www.dropbox.com/s/pcwrqg29xfrf7qu/dsDNA_20c.pdb?dl=0)

Thanks for your help,
Mahtab

4

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

5

Thank you very much

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