dock.xml

<ROSETTASCRIPTS>

		<SCOREFXNS>
			<ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep">
			</ScoreFunction>
			<ScoreFunction name="hard_rep" weights="ligand">
			</ScoreFunction>
		</SCOREFXNS>

		<LIGAND_AREAS>
			<LigandArea name="inhibitor_dock_sc" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
			<LigandArea name="inhibitor_final_sc" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
			<LigandArea name="inhibitor_final_bb" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
		</LIGAND_AREAS>

		<INTERFACE_BUILDERS>
			<InterfaceBuilder name="side_chain_for_docking" ligand_areas="inhibitor_dock_sc"/>
			<InterfaceBuilder name="side_chain_for_final" ligand_areas="inhibitor_final_sc"/>
			<InterfaceBuilder name="backbone" ligand_areas="inhibitor_final_bb" extension_window="3"/>
		</INTERFACE_BUILDERS>

		<MOVEMAP_BUILDERS>
			<MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="false"/>
			<MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="false"/>
		</MOVEMAP_BUILDERS>

		<SCORINGGRIDS ligand_chain="X" width="40">
			<ClassicGrid grid_name="classic" weight="1.0"/>
		</SCORINGGRIDS>

		<MOVERS>
			<Transform name="transform" chain="X" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
			<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
			<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
			<InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep" native="crystal_complex.pdb"/> 
		</MOVERS>

		<PROTOCOLS>
			<Add mover_name="transform"/>
			<Add mover_name="high_res_docker"/>
			<Add mover_name="final"/>
			<Add mover_name="add_scores"/>
		</PROTOCOLS>


</ROSETTASCRIPTS>