To run AutoDock on Windows, you must first download and install Cygwin, a Linux-like environment for Windows. Cygwin is available from http://www.cygwin.com. Follow the instructions for installing and setting up Cygwin from the Cygwin web site. There is also plenty of documentation about Cygwin.

ADT runs on Windows, out of the box.

Download the AutoGrid and AutoDock binaries for Cygwin: they are called autogrid4.exe and autodock4.exe (or autogrid3.exe and autodock3.exe, depending on which version you downloaded). For AutoDock 4, you will download a file called 'autodocksuite-4.2.1-i86Cygwin.tar.gz'; choose to "Save to Disk" if asked, and save it to your Desktop. Open a Cygwin terminal and type this:

      whoami

This will tell you what your username is. In the next command change YOUR_USERNAME to whatever whoami says your username is:

      cd /cygdrive/c/Documents\ and\ Settings/YOUR_USERNAME/Desktop

Now extract the files from the .tar.gz file:

      tar xvzf autodocksuite-4.0.1-i86Cygwin.tar.gz

These are in the directory bin/i86Cygwin. Copy the AutoGrid 4 and AutoDock 4 .exe files to the /usr/local/bin directory, by typing the following at the Cygwin terminal:

     cd i86Cygwin
     cp autodock4.exe /usr/local/bin
     cp autogrid4.exe /usr/local/bin

or for AutoGrid 3 and AutoDock 3:

     cp autodock3.exe /usr/local/bin
     cp autogrid3.exe /usr/local/bin

Now open a new Cygwin terminal, and type:

      which autodock4

or for AutoDock 3:

      which autodock3

This should find /usr/local/bin/autodock4 or /usr/local/bin/autodock3. You can now tell ADT to use AutoDock from /usr/local/bin/autodock3, and AutoGrid from /usr/local/bin/autogrid3.