1hzy_Funclib:XML

<ROSETTASCRIPTS>Dock the ensemble of ligand into the native structure using the Rosetta Score based affinities 

	<SCOREFXNS>
		<ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep">
			<Reweight scoretype="fa_elec" weight="0.42"/>
			<Reweight scoretype="hbond_bb_sc" weight="1.3"/>
			<Reweight scoretype="hbond_sc" weight="1.3"/>
			<Reweight scoretype="rama" weight="0.2"/>
		</ScoreFunction>
		<ScoreFunction name="hard_rep" weights="ligand">
			<Reweight scoretype="fa_intra_rep" weight="0.004"/>
			<Reweight scoretype="fa_elec" weight="0.42"/>
			<Reweight scoretype="hbond_bb_sc" weight="1.3"/>
			<Reweight scoretype="hbond_sc" weight="1.3"/>
			<Reweight scoretype="rama" weight="0.2"/>
		</ScoreFunction>
	</SCOREFXNS>
<LIGAND_AREAS>

Docking_Sidechains
<LigandArea name="dock_sc_B" chain="B" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_C" chain="C" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_D" chain="D" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_E" chain="E" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_F" chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_G" chain="G" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_H" chain="H" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="dock_sc_I" chain="I" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
Final_Sidechains
<LigandArea name="final_sc_B" chain="B" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_C" chain="C" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_D" chain="D" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_E" chain="E" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_F" chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_G" chain="G" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_H" chain="H" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_sc_I" chain="I" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
Final_Backbones	
<LigandArea name="final_bb_B" chain="B" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_C" chain="C" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_D" chain="D" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_E" chain="E" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_F" chain="F" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_G" chain="G" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_H" chain="H" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="final_bb_I" chain="I" 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="dock_sc_B"/>
		<InterfaceBuilder name="side_chain_for_final" ligand_areas="final_sc_B"/>
		<InterfaceBuilder name="backbone" ligand_areas="final_bb_B" extension_window="3"/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="true"/>
		<MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
	</MOVEMAP_BUILDERS>

Grid will be formed using the included chain so set ligand_chain to A, the protein chain 
	<SCORINGGRIDS ligand_chain="A" width="15">
		<ClassicGrid grid_name="classic" weight="1.0" atr="-1.0" rep="0.5" />
		</SCORINGGRIDS>

	<MOVERS>
              <StartFrom name="start_from" chain="B,C,D,E,F,G,H,I">
		     <Coordinates x="47.985" y="-4.913" z="28.027"/>
	      </StartFrom>
		<TransformEnsemble name="transform_ensemble" chains="B,C,D,E,F,G,H,I" box_size="50" move_distance="0.2" angle="20" cycles="1000" repeats="1" temperature="5" initial_perturb="5.0" use_conformers="true" optimize_until_score_is_negative="true" />
		<HighResEnsemble name="high_res_ensemble" chains="B,C,D,E,F,G,H,I" cycles="9" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking" rosetta="false" final_score="hard_rep" final_move="final"/>
	
 </MOVERS>
 <PROTOCOLS>
     <Add mover_name="start_from"/>
	 <Add mover_name="transform_ensemble"/>
	 <Add mover_name="high_res_ensemble"/>
 </PROTOCOLS>
</ROSETTASCRIPTS>