fff@bioinfo:~/rosetta_demos/Docking$ docking_protocol.linuxgccrelease @flags1 -database /usr/local/rosetta/3.1/rosetta_database
ERROR: Illegal value for real option -docking:dock_pert specified: 8
Post Situation:
fff@bioinfo:~/rosetta_demos/Docking$ docking_protocol.linuxgccrelease @flags1 -database /usr/local/rosetta/3.1/rosetta_database
ERROR: Illegal value for real option -docking:dock_pert specified: 8
What's in flags1? I think dock_pert needs two values, it may be erroring if you supplied only one.