You should have downloaded a file with a name such as "autodocksuite-4.2.1-i86Linux2.tar.gz" for Linux, and "autodocksuite-4.2.1-i86Darwin8" or "autodocksuite-4.2.1-ppcDarwin8" for Mac OS X.

At the command line, change directory to the directory where you downloaded the file, <download-directory> (Note: you should substitute <download-directory> with the full path to where the downloaded file is):

cd <download-directory>

Now let's extract the contents from the GNU-zipped tar file; in this example, we assume you have downloaded the Linux binaries:

tar xvzf autodocksuite-4.2.1-i86Linux2.tar.gz

This will create a new directory called "i86Linux2". In it, you will find two executables, called "autodock4" and "autogrid4". Let's change directory there first:

cd i86Linux2

Now move the executables to the directory where you normally keep your binaries. On Linux and Mac OS X, this is often /usr/local/bin. The main thing is that this directory is in your path.

mv autogrid4 /usr/local/bin
mv autodock4 /usr/local/bin

Now every time you open a new shell or Terminal, you should now be able to run AutoGrid 4 and AutoDock 4.