These AD manuals were provided by David Goodsell 1/17/2012:
4.0 from Nov 2 2005
4.1 from Apr 15, 2009
4.2 from Feb 25, 2010


Note:
AutoDock4.0_UserGuide.doc is 786KB and was originally named AutoDock4.0_UserGuide.MSWo~1.doc
AutoDock4.1_UserGuide.doc is 1MB and was originally named AutoDock4.1_UserGuide
AutoDock4.2_UserGuide.doc is 2MB and was originally named AutoDock4.2_UserGuide.doc

Updated in CVS March 2012:
4.2 from Nov 5, 2012 from AutoDock4.2.5_UserGuide20121105g.{doc,pdf}
