-in
 -file
  -s "inputs/protein.pdb inputs/ligands.pdb"
  -extra_res_path "prep/rosetta_inputs/"
-parser
 -protocol "inputs/dock.xml"
-packing
 -ignore_ligand_chi
 -ex1
 -ex2
 -flip_HNQ
 -no_optH false

-no_his_his_pairE
-overwrite
-mistakes
 -restore_pre_talaris_2013_behavior true 
