AutoDock library screening?

Dear AutoDock users:
 Is it possible to dock a virtual chemical library in .sdf format or any
 other format using AutoDock? Has anyone done it and are there
 Incidentally, a dumb question: why are binding free energies so
 high in docking scores compared to protein-protein delta Gs?
 Jeremy Jenkins
 Research Fellow
 Harvard Medical School
 jeremy_jenkins ^at^