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Problems with the RNA Denovo server

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Problems with the RNA Denovo server

I have problems using the RNA Denovo protocol on the web server. I try to get a structure for a duplex RNA, with a bulge, and the calculations fail, giving the error message: Protocol failed to produce any results! (File output/protein-0.out not found!)

As I have used this website before, and got results, I resubmitted an old calculation (that worked before), but that also fails. I have noticed that you have quite a lot of failed calculations on the RNA Denovo application recently. Have you changed anything, or am I doing anything wrong? I have submitted cuucuucguucucuu+aagagaauauaagaag, ((((((..(((((((+)))))))...)))))), not vary geometry, minimize RNA, allow bulge, don't use 2012 ff, 1000 structures to generate, 10000 Monte Carlo cycles, full run (Job 11928).


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Tue, 2014-11-25 01:45

Rhiju Das and I thank you for your post! We were able to debug the server issues, which were affecting several jobs, and kick off your runs again. The runs completed successfully, e.g.:

Please let us know if you run into further problems.


Wed, 2014-11-26 12:01

Thanks a lot for your help! :)
I really like ROSIE, especially since it is so difficult to get close to RNA structures in other ways.


Thu, 2014-11-27 01:30