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    I have run the command line with -help, the result is attached below.
    What do you mean in:file:s?
    It seems not in the list of options.

    $ /home/xxx/yyy/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease -help

    /home/xxx/yyy/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease [options]

    Options: [Specify on command line or in @file]
    in | | B| Input option group
    in: | | |
    termini | false | B| Put full N and C termini on input structures
    new_icoor | false | B| New set of idealized coordinates for full atom, 05-2009
    ignore_unrecognized_res | false | B| Do not abort if unknown residues are found in PDB file; instead, ignore them.
    remember_unrecognized_res | false | B| Ignore unrecognized residues, but remember them in PDBInfo.
    detect_disulf | false | B| Forcably enable or disable disulfide detection. When unspecified, rosetta
    conservatively detects disulfides in
    full atom input based on SG distance,
    but will not form centroid disulfides.
    Setting `-detect_disulf true` will
    force aggressive disulfide detection
    in centroid poses based on CB
    distance. Setting `-detect_disulf
    false` disables all detection, even in
    full atom poses. Note that disabling
    disulfides causes severe clashes for
    native disulfides.
    fix_disulf | | F| Specify disulfide connectivity via a file. Disulfides are specified as two
    whitespace-seperated residue indicies
    per line. This option replaces the old
    ‘-run:fix_disulf’ option.
    use_stupid_foldtree_format | false | B| use the fold-tree format that existed for one week after revision 21447