-in
	-file
		-s dock_input.pdb 
		# the input file should have two single, complete chains A and B
		# for Ab molecules (with L+H chains) use -docking::partners flag below
	-path
		-database /programs/l/rosetta/3.1-x86_64/rosetta_database/
		# customize this to point to your installation directory
-docking
	-randomize1
	# rotates partner1 (chain A) before docking proteins together 
	#-randomize2
	# rotates partner2 (chain B) before docking proteins together 
	#-partners 
	# defines docking partners by ChainID; see manual
-out
	-nstruct 10
	# this should be set to a large number for effective sampling
	-mute core.util.prof
	# reduces copious output, without overdoing as with -mute all
	-file
		-o dock_output
		# scorefile will be named dock_output.sc (or .fasc for fullatom)
		#-fullatom
		# fullatom is commented out for fast low-res "centroid mode" run
