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).
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.: http://rosie.rosettacommons.org/rna_denovo/viewjob/11909
Please let us know if you run into further problems.
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.