AMBER Archive (2008)

Subject: Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files

From: Robert Hanson (
Date: Thu Oct 09 2008 - 18:12:52 CDT

Very slick, Angel! Files loaded for me in about 5 seconds. I forgot that you
could zip up the data files. Of course!

Is there some way to differentiate "a water molecule" from the "water box" ?


On Thu, Oct 9, 2008 at 2:10 PM, Angel Herráez <> wrote:

> A working demo of this new feature is available at
> This uses today's latest 11.7.2dev version of Jmol.
> The Amber files sum up to 1.5 MB. I hope they run reasonably fast across
> the ocean.
> Thanks are due to Dr. Jesús Mendieta (from CBM in Madrid) for providing the
> files. They
> show the aminoacid residues involved in the catalytic centre of the Ras
> protein, together
> with GTP, Mg ion and a water molecule (in addition to the water box).
> Comments are welcome to
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
phone: 507-786-3107

If nature does not answer first what we want, it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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