ADL: ADT Error

Philip Crawford p.crawford at
Sun Jan 8 14:06:09 PST 2006

The Autodock executables, principally autogrid3 and autodock3 on Linux, are
in a separate download. You will need to request and obtain a license and
then you will be informed of the download location. See the AutoDock web

My practice with AutoDock (and other linux executables) is to create a
/usr/local/bin/Autodock directory and extract the .tar.gz file into that,
then create symbolic links from /usr/local/bin to the appropriate
executables under the Autodock/bin/Linux-whatever directory. The sym links
in /usr/local/bin are on the path. Of course you need administrator rights
(i.e., the root password) to do this.

When using AutoDockTools, you mainly need autogrid3 and autodock3, as the
other executables such as autotors, addsol, etc. have their functionality
performed by Python scripts in ADT.
Philip Crawford, B. Comp. Sc., MIEEE
School of Medical Sciences
The University of NSW
Phone: +61-2-9385 2564
Mobile: +61-419-294 698
Fax: +61-2-9385 1059
Email: p.crawford at

-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at] On
Behalf Of Mark Cunningham
Sent: Sunday, 8 January 2006 1:40 PM
To: autodock at
Subject: ADL: ADT Error

Hello All,

I made a new installation of AutoDock (1.2Beta version) onto RedHat 9 .  
When attempting to run autogrid3 from the autodocktools interface, I get the


              Xlib: extension
              missing on display ":0.0".
              "sh: line 1: autogrid3: command not found"

I am using the test files (system) from Scripps

Also, I have removed the stack limit with the: "ulimit -s unlimited" term in


It appears to be an issue of not finding the executables for autogrid3. How 
can I fix this problem? What is the executable for autogrid3? How do I put 
autogrid3 executables in the Linux path? Or how can I test (trouble shoot) 
to see if the autogrid3 executable is working?

Thanks for any and all help, been working on this for two days.


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