New ZINC database files in AutoDock "pdbqt" format are available at http://zinc.docking.org/pdbqt/. They have been tested with both AutoDock and the new AutoDock Vina. They are used in the Global Online Fight Against Malaria project and the FightAIDS@Home project on IBM's World Community Grid, but you can use them for any project you like.
Thanks to Stefano Forli, Ph.D., for preparing these pdbqt files! And thanks to Alex L. Perryman, Ph.D., for testing these files and sharing them with us!
Stefano and Alex are both members of Professor Art Olson's lab at The Scripps Research Institute in La Jolla, CA.