#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 '4K8F_A_HEM.pdb' -extra_res_fa HEM.params -out:path:pdb '/home/donruiz/cooa_project/ligand_docking/wildtype_4K8F/docking_2/output' #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