I try to design a protein named test.pdb. Each time, the fix bb will output the result as test_0001.pdb. Is there any way to output the result as design_0001 or any name? Thank you
There isn't a way to wholly replace the job name. The most efficient way to do this would be to symlink test to design like "ln -s test.pdb design.pdb" and run with design.pdb as the argument to -s.
There are various flags for moving where the output goes, but they aren't documented and don't work particularly well. This would let you put the output in some different (specially named) folder.