ZINC
This Link applies to: AutoDock 3, AutoDock 4
ZINC is a free database of commercially-available compounds for virtual screening, and a great source of input small molecules for AutoDock. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). For more details, see: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82.
Link: http://blaster.docking.org/zinc/