AutoDock and AutoGrid require Cygwin libraries for running, but since the version 4.2 it is not necessary to install the entire Cygwin environment anymore.

For this reason, there are now two ways of installing AutoDock under Windows.

Novice users are encouraged to follow the instructions for the Native Windows installation.

Users familiar with Unix-like environments that want to keep using the Cygwin/Bash environment can follow the instructions for the Cygwin Windows installation.

Native Windows installation (recommended)

1. Download the Windows installer (autodock4.x.x_win32.exe), double-click on it and follow the instructions
2. To test the installation, go to Start->Run... and type "cmd.exe". At the Windows prompt, type the command "autodock4" and if installation succeeded the terminal should report the following lines:
   

   Microsoft Windows 2000 [Version 5.00.2195]
   (C) Copyright 1985-2000 Microsoft Corp.
   
   C:\Documents and Settings\MGL>autodock4
   usage: AutoDock         -p parameter_filename
                           -l log_filename
                           -k (Keep original residue numbers)
                           -i (Ignore header-checking)
                           -t (Parse the PDBQT file to check torsions, then stop.)
                           -d (Increment debug level)
                           -C (Print copyright notice)
                           --version (Print autodock version)
                           --help (Display this message)

Cygwin Windows installation

1. Proceed with the native Windows installation.
2. Install Cygwin from the official web site. Follow recommended installation procedure for installing and setting up Cygwin or access to the documentation about Cygwin.
3. Open a Cygwin terminal and type the following command:
   

   cd /usr/local/bin

4. Either copy the AutoDock4/Autogrid4 binaries in this location:
   

   cp /cygdrive/c/WINDOWS/system32/autodock4.exe .
   cp /cygdrive/c/WINDOWS/system32/autogrid4.exe .
   

   or create a symbolic link:
   

   ln -s /cygdrive/c/WINDOWS/system32/autodock4.exe .
   ln -s /cygdrive/c/WINDOWS/system32/autogrid4.exe .
   

   Note for Windows2000 users: substitute "WINDOWS" with "WINNT" in the previous lines

5. Test the installation by opening a new Cygwin terminal and type the commands "autodock4" and "autogrid4":
   

   $ autodock4
   usage: AutoDock         -p parameter_filename
                           -l log_filename
                           -k (Keep original residue numbers)
                           -i (Ignore header-checking)
                           -t (Parse the PDBQT file to check torsions, then stop.)
                           -d (Increment debug level)
                           -C (Print copyright notice)
                           --version (Print autodock version)
                           --help (Display this message)
   
   $ autogrid4
   usage: AutoGrid         -p parameter_filename
                           -l log_filename
                           -d (increment debug level)
                           -h (display this message)
                           --version (print version information, copyright, and license)
   
   
   

   If you see the usage output, the installation has been successful.