-in
    -file
        -s 'PROT_LIG.pdb'
        -extra_res_fa COV.params

-out
    -prefix "ASx_"
    -file
        -scorefile score_ASx.sc      

-pH
    -pH_mode true 
    -value_pH 7.4

-run
    -ignore_zero_occupancy false

-parser
    -protocol dock.xml

-qsar
    -max_grid_cache_size 1
    -grid_dir qsar_grid

-jd2
    -delete_old_poses

-mistakes
    -restore_pre_talaris_2013_behavior true

-score
    -analytic_etable_evaluation true

-packing
    -ex1
    -ex2