tutorials/ligand_docking/answers/docking/options

#Pound signs indicate comments 

#-in:file:s option imports the protein and ligand PDB structures
#-in:file:extra_res_fa option imports the parameters for the ligand

-in
	-file
		-s '3PBL_A.pdb ETQ.pdb'
		-extra_res_fa ETQ.params

#the packing options allow Rosetta to sample additional rotamers for
#protein sidechain angles chi 1 (ex1) and chi 2 (ex2) 
#no_optH false tells Rosetta to optimize hydrogen placements
#flip_HNQ tells Rosetta to consider HIS,ASN,GLN hydrogen flips
#ignore_ligand_chi prevents Roseta from adding additional ligand rotamer

-packing
	-ex1
	-ex2
	-no_optH false
	-flip_HNQ true
	-ignore_ligand_chi true


#parser:protocol locates the XML file for RosettaScripts

-parser
	-protocol dock.xml

#overwrite allows Rosetta to write over previous structures and scores

-overwrite

#Ligand docking is not yet benchmarked with the updated scoring function
#This flag restores certain parameters to previously published values

-mistakes
	-restore_pre_talaris_2013_behavior true