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Thanks for the suggestion.
I moved -s down by one row. The flags is:
-dock_pert 3 8
-s /input/1brs.pdb
Now I got:
$ /home/xxx/yyy/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease @flags -database /home/xxx/yyy/Rosetta3.1/rosetta_database/
ERROR: Option matching -dock_pert not found in command line top-level context
I also run:
$ /home/xxx/yyy/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease -help
the output is:
Usage:
/home/xxx/yyy/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease [options]
Options: [Specify on command line or in @file]
…….
It seems flag can’t be recognized by docking_protocol.cygwingccrelease, am I right?