Reply To: I’m a total beginner to Rosetta 3.2 and there are no tutorials for me to follow. Can someone help.? =)

[Anonymous]

This will copy one of the docking demos and run it for you. I can’t give you the correct paths, you’ll have to fix those.

cp -r (whatever)/rosetta_source/test/integration/tests/docking_full_protocol wherever/you/want/to/put/it
cd wherever/you/want/to/put/it
cat flags (then read the flags to see your answer for a command line)
path/to/rosetta_source/bin/docking_protocol.linuxgccrelease @options -database path/to/rosetta_database/

The @flags syntax allows you do put all the command line flags into a file, instead of cramming them onto the command line itself. The PDB input is passed in via the “-s” flag. You’ll note the input already contains both receptor and ligand. For this trivial input, they start out already docked, but you can just concatenate your two PDBs and that will work fine as a starting structure. (The spin flag tells Rosetta to randomize the orientations of the input chains, so Rosetta is not “cheating” by starting at the correct answer in this demo).