Internal Server Error

Dear all,

I am using Multibody interface of HD2.2 for water refinements and get an Internal Server Error since yesterday. I have tried to submit calculations from 3 different networks using Chrome and Firefox.

Yesterday I could submit a couple of calculations, but at some point I got an error message:
IOError: [Errno 28] No space left on device
And afterwards all the time: Internal Server Error

I would be very grateful for your help and advice about what can be the reason of this error.

We don’t see any space issues. We restarted the server services.
Please give it another try.

Dear Alexandre,

Thank you very much, now it works perfectly again.

I would like to ask if it is possible that after restart of the server yesterday my submitted jobs were removed or somehow paused by HD2.2?
One of my jobs finished yesterday at 20:40 and since that time non of my calculations finished, although before I was receiving around 8-10 completed calculations per day and I had around 50 queued submissions.

Thank you for your time.

Hi Marija

There were issues with the grid last night. These have been resolved by now.
Runs should be progressing again.

Thank you very much.

Dear Alexandre

I have a student who started a run on the HADDOCK 2.2 webserver on Monday (9th Nov). This had progressed to it1 37% but has been stalled at this point since last night. The student has started a new run but I expect that this won’t start because the previous run is still open. Is it possible to stop the first run which is stalled so the second run can start? Or can the first run be pushed to start progressing again?


Kayleigh Walker

There have been grid issues since a few days that have caused problems.
This should now be solved - but not really under our control.

The grid infrastructure we are using to run jobs is a complex system, not under our control.

PS: Grid submission has resumed and the runs should start progressing again.

Thanks for the quick response! Just to clarify, its not an issue that the run hasn’t started up again yet? It will progress if we give it time?

I appreciate we are using a free service and need to be patient. Thanks for your time

I can see the run has started progressing! Thanks :slight_smile:

Dear Alexandre,

I am using the easy interface of Haddock2.2 for protein-DNA docking. But after I submitted the structures of the two molecules, I got the internal server error like this:

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.

More information about this error may be available in the server error log.

Could you help me or give me some advice?Thanks!

Hi Han

We had to restart the web server.
Please try again.

Good morning, since yesterday I have a problem, I have tried to verify the status of an odcking job and the following message appears:

Internal Server Error

The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.

I can access completed runs fine on our side.

Are you referring to the 2.4 HADDOCK server?

Can you share (via email) a runID / URL ?

Good morning, yes, I did the docking by HADDOCK 2.4. I have run the job three times. Thank for tour help. I Will stay tuned.

This is a strange issue.

In any case you can download your runs by simply adding .tgz to the URL.

Unpack the archive and look into the results directory.

You will find a file called clusters_haddock-sorted.stat_best4 which contains cluster stats and you will also find PDB files of the top10 clusters.

However looking at your run (the ADN1) it seems that the molecules did not dock (which could explain the post-processing issue).
Something is wrong in the way you defined restraints (if any)… Also you DNA is taken apart.
You should define it as a single molecule with the two strand renumbered if needed to avoid overlap in residue numbering.

Thank you very much for your reply.
I have tried to do it with both strings but always get this message.

Error in PDB file. Your PDB contains multiple chains with overlapping numbering: C1 - E1 Consider selecting a chain or splitting your PDB

For this reason I separate them

Check some of our tutorial on the site…

You will have to renumber the second chain. Our PDB-tools server can be used for that.


Separating the chains won’t make the docking work… waste of CPU :slight_smile:

I have tried to use the tool but it does not run,  maybe I am not enabled to use it.