The scripts and input files that accompany this demo can be found in the demos/public directory of the Rosetta weekly releases.

KEYWORDS: LIGANDS DOCKING

To run: (where $ROSETTA3=path-to-Rosetta/main/source)

$> $ROSETTA3/bin/ligand_dock.default.linuxgccrelease @flags

Real run has nstruct 500 e.g. and run 10 separate runs for 5000 total runs.

Gives output: .l silent.out

To extract the scores, run this:

$> $ROSETTA3/src/apps/public/ligand_docking/get_scores.py silent.out > scores.tab

Then you can extract a structure:

$> $ROSETTA3/bin/extract_atomtree_diffs.default.linuxgccrelease @flagsextract

Here there's only one structure and one tag for that structure. In a real case you'd have many more:

$> $ROSETTA3/src/apps/public/ligand_docking/best_ifaceE.py -n 1 silent.out

For more information, see the ligand dock entry in the manual:
http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_ligand_docking.html