Hi I have not used Rosetta for a while. i wanted to relax my receptor for enzyme design and i kept on having the message
Evaluation Creator active ...
protocols.relax.FastRelax: WARNING: Pose has no residues. Doing a FastRelax would be pointless. Skipping.
protocols.jd2.JobDistributor: S_0001 reported success in 0 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs att
here is my flag file
-s ligand.pdb #-s your_structure.pdb
It used to work before, dont know why it does not work now.
It looks like you forgot to put the reference to the options file on the Rosetta command line. Rosetta does not auto-load any options files, if you're using them, you have to manually specify them on the commandline with the '@' syntax. E.g.
The error messages you're getting are consistent with not passing any input options, which would be the case if the options file isn't being read.