To configure the global parameters, change into [Protégé-dir]/plugins/edu.stanford.smi.protegex.storage.rdfdb directory and type java -jar prdfdb_config.jar. Click on the Load menu item. This should load the default values from the file protege_rdfdb.settings. Change these parameters appropriately. Save the settings with the Save menu items and quit. If you have have not changed any of the default configurations and set up MySQL as previously mentioned, you do not need to change any of the settings.