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

[Anonymous]

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?