Personal tools
You are here: Home Obtaining
Document Actions

Obtaining AutoDock

by morris last modified 2007-05-07 15:07

How to obtain AutoDock, and information on supported platforms.

 

Academic Availability

AutoDock 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 AutoDock to commercial institutions. Contact Art Olson for more information.

How is AutoDock distributed?

AutoDock 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 AutoDock 4 beta?

AutoDock 4 is now available on a limited basis for beta testing. A selected number of users will be given a license for AutoDock4 beta. In order to be considered for a beta license, please send e-mail to Prof. Arthur Olson (olson@scripps.edu), stating your prior experience with AutoDock and your willingness to provide user feedback during the beta test period. If approved you will then be sent the license to complete and return. We will consider licenses for commercial companies for evaluation purposes only. Once the beta test period is over, AutoDock 4.0 will become generally available.

How do I obtain AutoDock?

  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: wetjen@scripps.edu. 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

Mail:

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

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 http://www.gnu.org/order/ftp.html, 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):

Company

Architecture

OS

Power Macintosh G3, G4 and G5
Alpha
  • OSF

Precision Architecture
  • AIX 5.2
  • SuSE SLES 8
Generic

x86 (IBM PC Clones)

MIPS

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

 

How do I run AutoDock at Scripps?

If you work at Scripps, you can use the latest version of AutoDock that lives under the /mgl/prog and /bluefish/people-b/applications/autodock directories.  You do not need to sign a license agreement.

AutoDock and AutoGrid run on many platforms, including Darwin, IRIX64, Linux, Mac OS X, Solaris and Windows/Cygwin. They are also available on the Linux Compute Cluster bluefish, where you can run many AutoDock jobs simultaneously.  This is an excellent resource for virtual screening.

The bluefish machines currently run the PBS batch queuing system.

If you have a laptop, and you want to run AutoDock using a local copy, you should copy the appropriate AutoDock and AutoGrid executables (autogrid3+autodock3 or autogrid4+autodock4) to your laptop:

Linux: /mgl/prog/i86Linux2/bin/auto{dock,grid}[34]

Mac OS X 10.4 / Intel: /mgl/prog/i86Darwin8/bin/auto{dock,grid}[34]

Mac OS X 10.4 / Power PC: /mgl/prog/ppcDarwin8/bin/auto{dock,grid}[34]

Windows / Cygwin (see FAQ): /mgl/prog/i86Cygwin/bin/auto{dock,grid}[34]

If you need help, or have a request for a new feature, let me know and I will make sure that your question is answered as soon as possible.

Garrett M. Morris

 

(1) The machine you wish to run AutoDock on should be able to automount  /mgl and its sub-directories. Check if you can do this:

% cd /mgl/prog

If you can, then you go to step (2).  If not., you will have to install a local copy on your machine.

(2) If you want to know what type of platform your machine is (i.e. hardware and operating system versions, etc.), type:

% uname -a

(3) You should copy the .autodocksetup file to your home directory:

% cp /home/garrett/.autodocksetup $HOME

(4) Next, in your .login file, add these lines and uncomment the appropriate ARCHOSV line for your platform (by deleting the "#" character at the start of the line):

#setenv ARCHOSV i86Linux2  #Linux on an Intel x86.

#setenv ARCHOSV ppcDarwin6  #Darwin 6 & Mac OS X 10.2 (Jaguar).

#setenv ARCHOSV ppcDarwin7  #Darwin 7 & Mac OS X 10.3 (Panther).

#setenv ARCHOSV ppcDarwin8  #Darwin 8 & Mac OS X 10.4 (Tiger).

#setenv ARCHOSV sgi4DIRIX646  #SGI IRIX64.

source $HOME/.autodocksetup

set path = ($path  $AUTODOCK_BIN $AUTODOCK_UTI)

This should set up everything you need to use AutoDock and its related programs ($AUTODOCK_BIN) and scripts ($AUTODOCK_UTI).  

If you are running on the bluefish cluster then add this to your .login file (in the Linux section if you have one):

set path = ($path /bluefish/people-b/applications/autodock $AUTODOCK_UTI)

(5) Now you are ready to get started.  Download a PDF version of the AutoDock User Guide and print it out, or read it online.

If you do not have time to read documentation (and you really should...), jump right to the "Getting Started" section of the User Guide. 

Note that on the bluefish cluster, you can launch several AutoDock jobs at once using the "submit.py" script, and while the dockings are running or when they're finished, you can cluster the results using "recluster.py" into one large histogram. If you already have a DPF with the name "stem.dpf", and you want to run on ncpus CPUs, where ncpus is an integer, say 10 or 20, then type this:

% submit.py stem ncpus

To re-cluster the dockings, use ADT, or on the command-line on bluefish the usage is:

% recluster.py stem num ['during'|'end'] [rmstol]

For example:

% recluster.py z3 20 during 3.5


So here, z3.dpf is the name of the DPF, 20 is the number of concurrent docking jobs you want re-clustered, during means that results produced during the dockings will be used, and 3.5 is the RMSD tolerance in Angstroms for re-clustering. Note that recluster.py is dependent on you using submit.py to start the jobs, since it makes the same assumptions about file naming conventions.

Happy docking!

Garrett M. Morris

Related content

Powered by Plone CMS, the Open Source Content Management System

This site conforms to the following standards: