AMBER Archive (2008)

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

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Thu Oct 09 2008 - 11:30:32 CDT

Jmol 11.7.2 now reads the AMBER_ATOM_TYPE line in topology files and
incorporates that as the "type" of the atom, which can be displayed using
the %B descriptor in a label (sorry, all the reasonable single-letter
descriptors are taken!) or used as a selector using the WITHIN syntax. For
example:

   select within(type, "CT")
   display not within(type, "HW,OW")

see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
working version is at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip

Bob Hanson

ps: What is R.E.DD.B ?

>> Can Jmol display force field atom types available in Tripos mol2 files,
>> AMBER prmtop files or in CML files ? This would be great, & we would add
>> this new feature in R.E.DD.B...
>>
>> Thank you, regards, Francois
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> 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
> 

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
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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