The commandline is:
$/home/xxx/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease @flags -database /home/xxx/Rosetta3.1/rosetta_database/
The content of flags is:
-s /input/1brs.pdb (I also tried various formats and locations of directories for 1brs.pdb, none of them worked)
-dock_pert 3 8
-mute core.util.prof ## dont show timing info
Before getting this error message in running rosetta, I had many troubles in the installation.
Luckily, these troubles were solved by following the discussion between Marsia and smlewis.
(see: problem compiling rosetta3.1 in windows vista 32 bit using cygwin 1.7.5-1)