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
>
>
>
>
>
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Received on Sun Aug 26 2007 - 06:07:40 PDT
