“ERROR: Unable to open file: ./silent.out”
I would guess you are running the test in a directory for which you do not have write permission. Rosetta is saying it can’t write to that file; probably you don’t have write access to the directory you’re running in.
“ERROR: Option matching -dock_mcm not found in command line top-level context”
The documentation is out of date. I believe dock_mcm is the default, so you no longer need to specify it. If you’ll examine rosetta_source/test/integration/tests/docking instead, you’ll see that the option is commented out in the flags file for that test.