The database contains common parameters and settings that are not specific to a particular system.
You are responsible for telling the Rosetta application where the database can be found (e.g., with the flag -database ). A convenient alternative is to set the ROSETTA3_DB environment variable in your .bashrc or .cshrc. Bash-users, for instance, would insert the line export ROSETTA3_DB=$HOME/rosetta/rosetta_database if they had installed the rosetta distribution in their home-directory.