-in:file:s "./input_files/dock_design_test_Est_CHba_apo.pdb ./input_files/D2N.pdb" 
-extra_res_fa ./input_files/D2N.params
-out:file:scorefile dock_design_test_D2N_Est_CHba.sc 
-score:weights beta_nov15
-ex1  
-ex2 
-no_optH false  
-flip_HNQ true  
-ignore_ligand_chi false 
-parser:protocol ./input_files/ligand_dock_design.xml 
-nstruct 5
-overwrite 
