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Obtaining AutoDock3

by morris last modified 2009-05-18 15:40

How to obtain AutoDock, and information on supported platforms.

Academic Availability

AutoDock3 continues to be free to academics and educational institutions for non-commercial use.  The C and C++ source code of all the programs is provided, along with Unix makefiles to help compile the executables.  You and an institutional representative, such as your Head of Department, are required to sign and return a Software Distribution Agreement.  Then you will be sent instructions by email on how to download the software from The Scripps Research Institute. There are more details below.

Commercial Availability

The Molecular Graphics Laboratory currently distributes AutoDock3 to commercial institutions. Contact Art Olson for more information.

How is AutoDock3 distributed?

AutoDock3 is distributed only after you have read, signed and returned a Software Distribution Agreement. You are then sent, by email, ftp instructions on how to download the source code across the internet. We do not distribute AutoDock through traditional mail.

How do I obtain AutoDock3?

  1. Download the License Agreement, Read and Sign It
  2. Fax and Mail the Signed License Agreement
  3. Wait for instructions

1. Download the License Agreement, Read and Sign It

If you have a PostScript printer and Adobe Acrobat Reader, you can download the license agreement here:
( to donwload the file right click on the link and select "save link as" )

Version North America Europe
AutoDock 3.0 PDF 8.5" x 11" PDF A4

and print it out. The agreement is available in both North American and European paper sizes, in PDF (Portable Document Format). Both Acrobat Reader and the PDF-displaying plug-in are free and available from Adobe Systems Incorporated.

If you cannot print these files, you can obtain the agreement by sending email to Melissa Wetjen, Office of Technology Development, Phone: (858) 784-8496 or Email: Please include your daytime telephone number, your FAX number and your address. It is important to include your FAX number, because you will be faxed a copy of the software distribution agreement.

Read the license agreement. If you agree to its conditions, fill out the form clearly using a typewriter or block capital letters. You must sign the form, and you must have your institutional or departmental head also sign it.

2. Fax and Mail the Signed License Agreement

Once the Software Distribution Agreement has been completed and signed, please fax and mail it with the letter of interest to the fax number and address below:

Fax Number:

+ 1 (858) 784-9910

Telephone Number:

+ 1 (858) 784-8496


The Scripps Research Institute
Office of Technology Development
10550 N. Torrey Pines Rd., TPC-9
La Jolla, CA 92037-1000

3. Wait for the download instructions

You will be sent instructions by email, once we receive your completed Software Licence Agreement. Please allow 5 business days for processing.

Please read the instructions carefully: they will explain everything you need to know.

Once you have downloaded the distribution and un-compressed the files, please read the "README" files in each directory: they contain important instructions and information.


How big is AutoDock?

AutoDock is distributed in the form of a Gnu-zip (gzip) compressed tar file, which contains the source code, binaries, examples, utilities and Makefiles. The Gnu gzipped file for AutoDock 3.0, extension ".gz", is very large: about 11 Mbytes. It contains two sets of grid maps along with several binaries for different machines and operating systems. The Unix "compress" command refused to compress the orignal tar file, which was about 15 MBytes, so only the gzipped version is provided. Gnu-zip or gzip can be downloaded for free from a variety of sites, including, although you are encouraged to make a donation to the Free Software Foundation if you can. Once you have downloaded the file you will have to "gunzip" and "tar xvf" it. Binaries are included for Silicon Graphics IRIX 5 and 6, Compaq/DEC Alpha OSF1 Unix and Sun Solaris. Some of the utilities require that you uncomment certain lines in the Makefiles to match your hardware, and then run "make", in order to generate the executables. Detailed instructions will be provided when we receive your license agreement: see below.

Which platforms does AutoDock run on?

AutoDock has been compiled succesfully on the following hardware platforms, all running the Unix operating system (unless otherwise stated):




Power Macintosh G3, G4 and G5
  • OSF

Precision Architecture
  • AIX 5.2
  • SuSE SLES 8

x86 (IBM PC Clones)


If anyone has compiled AutoDock on another system, please let me know so I can keep this list up-to-date.


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