AMBER Archive (2007)

Subject: AMBER: NETCDF

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Fri Aug 24 2007 - 08:03:37 CDT

Sorry - start with ncdump....

I should have recommended you try ncdump, which you will find in the bin
directory of your netcdf build:

~/whereveryoubuildamber/src/netcdf/bin/ncdump 151-200.crd | head -40

netcdf 151-200 {
dimensions:
        frame = UNLIMITED ; // (50 currently)
        spatial = 3 ;
        atom = 8855 ;
        label = 5 ;
        cell_spatial = 3 ;
        cell_angular = 3 ;
variables:
        char spatial(spatial) ;
        float time(frame) ;
                time:units = "picosecond" ;
        float coordinates(frame, atom, spatial) ;
                coordinates:units = "angstrom" ;
        char cell_spatial(cell_spatial) ;
        char cell_angular(cell_angular, label) ;

// global attributes:
                :title = "" ;
                :application = "AMBER" ;
                :program = "sander" ;
                :programVersion = "9.0" ;
                :Conventions = "AMBER" ;
                :ConventionVersion = "1.0" ;
data:

 spatial = "xyz" ;

 time = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0 ;

 coordinates =
  67.871, 87.953, 51.624,
  68.141, 87.77, 50.668,
  67.508, 88.891, 51.528,

> Dear Amber users,
>
> I have recently been using the NETCDF trajectory format in AMBER and
> decided not only are they easier to handle but process much faster in
> other programmes such as ptraj.
> However, after converting an ASCII trajectory into a NETCDF
> trajectory I find that whenever it is subsequently processed in ptraj
> I get the following message :
>
>
> Whoa Nellie & Cripes!!! We should see 'x', 'y' and 'y' characters in
> the spatial variables of the AMBER NetCDF trajectory file unless
> someone altered the spec. We see '', '' and ''
>
> The processed trajectory does not seem to have problems but I was
> wondering if anyone else has come across this?
>
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu