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How do I run AutoDock at Scripps?

This How-to applies to: AutoDock 3
This How-to is intended for: User

instructions to run AutoDock at The Scripps Research Institute.

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.


(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!

by gillet last modified 2007-05-22 12:29

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