I recently presented an AutoDock tutorial at the EBI based around PyRx 0.8, an impressive GUI for AutoDock and Vina by Sargis Dallakyan. It worked out very well, and a big thanks to James Watson from the EBI who helped install all the software. While PyRx still has a few rough edges, it is an order of magnitude easier to use than the existing AutoDock GUI AutoDockTools (although the latter allows more fine-grained control).
We followed the 2010 PyRx tutorial (PyRx2010_rvsnALP_7122010.pdf) available from http://pyrx.scripps.edu/SI/2010/. You will also need the 3D.sdf from that location. You may also want to download sample.tar.gz.
The following notes describe how to get everything set up on Windows:
(1) Download AutoDock 4.2. When installing, install to "C:\Program Files (x86)\AutoDock" not C:\Windows\system32 as suggested.
(2) Download and install PyRx 0.8. This installs to "C:\Program Files (x86)\PyRx".
(3) Replace the appropriate file in "C:\Program Files (x86)\PyRx\Lib\site-packages\PyRx" with importWizard.py, dbPlot.py and autodockNavigator.py.
(4) Have everyone start PyRx (there should be a shortcut on the desktop, else run PyRx.bat) and under Edit/Preferences set the location of AutoDock to "C:\Program Files (x86)\AutoDock\autodock.exe" (they can just browse to the folder and file), and similarly for AutoGrid. If they did this properly, the "Local" radiobutton in the bottom of the AutoDock Wizard tab should be available. They should choose this during the docking.
It should then be possible to work through the tutorial without problems. The tutorial involves docking a single molecule with AutoDock, then running a virtual screen with Vina (I recommend only choosing 5 molecules unless you have lots of time on your hands).
Note that pdbqt files, configuration files and such are saved into C:\Users\MyName\.mgltools\PyRx, if you want to have a look. You can delete this folder to reset PyRx. And all of this software should work equally well on Mac and Linux, although I haven't tested this.