-parser:protocol low_res_docking.xml
 
-s 2VYR_input_low_reso.pdb
 
-docking
	-dock_pert 8 5 
	-spin 1
	-randomize1
	-docking_centroid_outer_cycles 10
	-docking_centroid_inner_cycles 50
-docking:dock_mcm_trans_magnitude .1
-docking:dock_mcm_rot_magnitude 1

-native 2VYR_input.pdb 

-nstruct 10 

-database mini_current_checkout/minirosetta_database/ 

-linmem_ig 10 

-ex1 

-ex2 

-ex1aro 

-overwrite

-packing:repack_only

-out:pdb 

-use_input_sc
