Hello:
I am trying to relax my protein with following parameters, but it failed with messages:
-database /home/albert/install/rosetta_2014/main/database
-nstruct $nstruct
-in:file:s $pwd/input.pdb
-relax:quick
-out:path:pdb .
-out:suffix $i
-out:file:fullatom
-out:pdb
core.pack.task: Packer task: initialize from command line()
protocols.jd2.JobDistributor:
[ERROR] Exception caught by JobDistributor for job nvt0_0001AHH IT'S THE END OF DAYS. RUN FOR YOUR LIVES
protocols.jd2.JobDistributor:
protocols.jd2.JobDistributor: nvt0_0001 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy /home/albert/Documents/project/mEGOR_screening/03-mechanism/loop/nvt.pdb
protocols.jd2.JobDistributor:
[ERROR] Exception caught by JobDistributor for job nvt0_0002AHH IT'S THE END OF DAYS. RUN FOR YOUR LIVES
protocols.jd2.JobDistributor:
protocols.jd2.JobDistributor: nvt0_0002 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 2 jobs considered, 2 jobs attempted in 1 seconds
You're getting that error message because you didn't specify a loops file.
I'm not sure why it would be looking for a loops file, though. From the options you posted, the relax application shouldn't need a loops file. What's the commandline that's printed in the very top of the log which shows this message? (It looks like it may be different from what you're expecting, as the log looks like it's working on a file called "nvt.pdb" rather than "input.pdb".) Also, are you using the relax application (e.g. relax.default.linuxgccrelease") or are you doing the relax through some other method?