AMBER Archive (2008)

Subject: RE: AMBER: coordinate file question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Sep 30 2008 - 08:55:57 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Robert Hanson
Sent: Tuesday, September 30, 2008 6:30 AM
To: amber_at_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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Robert Hanson
Sent: Monday, September 29, 2008 8:16 PM
To: amber_at_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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