-run
 -constant_seed
 -rng mt19937
-in
 -file
  -s ligand_dock/7cpa_input.pdb
  -native ligand_dock/7cpa_native.pdb
-out
 -file
  -atom_tree_diff atom_tree_diff.out
 -overwrite	
-packing
 -no_optH
 #-ex1
 #-ex1aro
 #-ex2
-jd2
 -dd_parser true
-parser
 -protocol ligand_dock/ligand_dock_script.xml

-mute core.util.prof ## dont show timing info
-mute core.io.database
