Im using Rosetta CM based on this tutorial: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM. I run the jobs in batches of 1000 and most of them don't complete all 1000 because of a "Cannot normalize xyzVector of length() zero" although they did complete anywhere between 60 and 300 before quitting. From some quick searches it seems like this is due to a unlucky random seed pick, so I was wondering if there was any way to tell rosetta to ignore the error and restart that job or skip it.
I tried using "-in:file:skip_failed_simulations true" and "-jd2:failed_job_exception false" by creating a bad input pdb and ran it through score_jd2 to test if those would work but they didn't seem to do the trick. Any suggestions would be greatly appreciated.