Subject: Re: CCL:Autodock tools under LINUX (success)

From: "Garrett M. Morris" <[email-masked]>
Date: Tue, 2 Jul 2002 18:23:58 -0700

Hi Carlos,

I read your post on the CCL about AutoDockTools on Linux.  I'm happy
you figured out what your problem was with your Operating System.  
Have you actually tried using AutoDockTools?

On Tue, 2 Jul 2002, Dr. Carlos F. Marcos wrote:

> 
> Hi, everybody. I've sent a message a couple of days ago regarding
> a problem trying to run AutoDockTools under Linux. Thanks so much
> to all that have answered my question. I could successfully solve
> the problem just by installing in my system the necessary OpenGL
> graphic libraries, which come in a packet called Mesa. On the othe
> hand, Chris wrote that he found the autodock tools "quite bad and
> highly unstable". Can anyone suggest an alternative to do flexible
> docking under Linux? Have a nice day

I was curious to know who "Chris" is, your reply to CCL did not
explain who he was or which version of AutoDockTools he had used and
on which platform.  We have never heard from Chris about his
experiences, and we would love to hear from him, in particular what
gave him the impression that ADT was "quite bad and highly unstable".

We have a large number of people using AutoDockTools quite happily
here at Scripps and elsewhere around the world.  Any feedback is
always welcome, so that we can make future releases better.

Furthermore, I would appreciate you making a distinction in your
discussions in public fora like the CCL, between "AutoDock" and
"AutoDockTools" (ADT).

AutoDock is a standalone computational package, that does not have,
and does not require a GUI to run.  It is very stable and well tested.  
AutoDock has been distributed to more than 1600 sites around the world
in the last decade, and there are more than 300 publications in the
literature citing its successful use.  AutoDock is under active
development, and its popularity is continuing to grow.

AutoDockTools is a Graphical User Interface (GUI) and is relatively
new, having been distributed in just the last couple of years.  It is
still evolving and being developed, chiefly by Ruth Huey, and builds
upon the terrific Python Molecule Viewer (PMV) developed by Michel
Sanner, also here at Scripps.  The ADT GUI helps to make AutoDock
easier to use.

AutoDockTools is *not* required to run AutoDock.  Even if you cannot
get AutoDockTools to run on your particular flavour of operating
system, AutoDock will still run without problems, and you can still
carry out flexible docking.  The User Guide distributed with AutoDock
explains in great detail how to do this.

I hope this clears up any misconceptions, and I look forward to
hearing from you about your posting and experiences,

Best wishes,

Garrett

___
Dr Garrett M. Morris, MA, DPhil
The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: [email-masked]
La Jolla,  CA 92037-1000,  USA.       www.scripps.edu/pub/olson-web/gmm