Hi Robert,
Yes the IFBOX in the prmtop should tell you whether to look for the box or
not - other programs like VMD just have two input formats to choose from -
AMBER Coordinates and AMBER Coordinates with Box.
Good luck,
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Robert Hanson
Sent: Tuesday, September 30, 2008 6:30 AM
To: amber.scripps.edu
Subject: Re: AMBER: coordinate file question
Thanks, Ross,
Great. That seems to work now.
To be clear: It's the IFBOX parameter = 1 that determines that? (Files from
some sources I see do not have that extra point.) So if IFBOX == 0, then I
should not have the box size?
Bob
On Mon, Sep 29, 2008 at 10:33 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
Hi Robert,
The last coordinate is the box dimensions. Coordinate files come in multiple
flavors.
1) inpcrd file
Gas phase - should contain 3*natom
Orthorhombic periodic - should contain 3*natom +
xbox,ybox,zbox,alpha,beta,gamma
where alpha,beta,gamma = 90.0
truncated octahedral periodic - should contain 3*natom +
xbox,ybox,zbox,alpha,beta,gamma
2) restart file. As inpcrd file but contains 3*natom + 3*velocity +
box.....
3) mdcrd file (fomatted) - 3*natom + xbox,ybox,zbox
4) mdcrd file (netcdf binary) - see
http://ambermd.org/netcdf/nctraj.html
Also see
http://ambermd.org/formats.html
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Robert Hanson
Sent: Monday, September 29, 2008 8:16 PM
To: amber.scripps.edu
Subject: AMBER: coordinate file question
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
--
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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Received on Wed Oct 01 2008 - 05:10:49 PDT
