-in
	-file
		-s ../3-clean_pdbs/2Q5K_mutant_with_ROC.pdb
		-extra_res_fa ../2-Saquinavir/1-from_ideal/ROC.params
-out
	-nstruct 2
	-file
#		-atom_tree_diff atom_tree_diff.out
# -mute all
#	-mute core.util.prof ## dont show timing info
	-mute core.io.database
-packing
	-no_optH
	-ex1
	-ex1aro
	-ex2
-parser
	-protocol ligand_dock.xml

