AMBER Archive (2008)

Subject: AMBER: coordinate file question

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Mon Sep 29 2008 - 22:16:25 CDT

I'm setting up Jmol to read Amber topology / coordinate files. But I've run
into an odd snag. It seems the coordinate files that I have has one too many
coordinates. I'll send links to the files if necessary, but does it make
sense that a topology file reading

%FLAG
POINTERS
%FORMAT(10I8)

   37300 16 29669 6234 12927 6917 28267 6499
0 0
   87674 9013 6234 6917 6499 47 101 41
31 1
       0 0 0 0 0 0 0 1
24 0
       0

has a coordinate file that contains blocks of 37301 * 3 coordinates?
Does the last coordinate somehow mean something other than an atom? Do these
parameters somehow indicate that an additional coordinate is present?

Thanks,

Bob Hanson 

-- 
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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