That sounds like you are having file system permission problems. If the file system is refusing Rosetta access, it will fail to find inputs/D2N_aX.params, and it will fail to know if the ??_0001.pdb file already exists (leading to the -overwrite warning).
Are you running from within the Rosetta source you installed? Try copying out the demo folder to a separate location, checking the permissions, and running from there.
I am somewhat concerned that you are running as root; Rosetta doesn’t require it (although installing to /usr/local might). I always have 10 copies of Rosetta anyway so I’ve never tried installing in that fashion.