Reply To: ERROR: Option matching -s not found in command line top-level context

[Anonymous]

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.

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

Usage:
/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
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