Using ensemble pdb not working on web server

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 ( and submit a single structure, haddock works. If we submit the original or reassembled ( ensemble haddock fails. The log for the latter can be found at
We have made sure that the pdbs are in the correct format using
Any help would be greatly appreciated.

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

Thanks to your response.
I checked my pdb again and it was not empty.
I submitted the same pdb again and it failed again (
This is the link to the pdb file I used.(

Thanks for your help,

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.

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.


Thank you very much

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