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Frequently Asked Questions (& Answers!)

Installing AutoDock

How do I install AutoDock on Linux and Mac OS X?

I've downloaded the tar.gz file containing the AutoDock and AutoGrid executables. How do I install them?

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.

Note: you have to have administrative privileges to do it (either switching user to root or by using sudo).


As root:
mv autogrid4 /usr/local/bin
mv autodock4 /usr/local/bin
As regular user (you have to type your user password):
sudo mv autogrid4 /usr/local/bin
sudo 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.

This FAQ applies to: AutoDock 4

Problem with libstdc++.so.6 on Linux

What to do if you are getting "libstdc++.so.6: cannot open shared object file: No such file or directory" error message.

You'll need either to build autodock from source or install the missing library. Since libstdc++.so.6 comes preinstalled with the latest Linux systems, in this case, it would be better to build autodock from source.

See also: http://mgldev.scripps.edu/pipermail/autodock/2009-June/005997.html

by morris last modified 2007-07-19 17:31
Contributors: Ruth Huey, Garrett M. Morris, Sargid Dallakyan, Stefano Forli

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