Hi Chris,
Thanks for your response the ncdump of the trajectory in question lis
below (I have one line where there seems to be a problem):
I have had no other problems with reading and writing netcdf files on
a number of different platforms that I use here so I assume something
happened to this file in particular.
I still think that no problem fundamental corruption with the file,
once it is processed it looks fine in VMD, for instance.
Cheers, Geoff.
netcdf traj {
dimensions:
frame = UNLIMITED ; // (3907 currently)
spatial = 3 ;
atom = 43638 ;
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) ;
double cell_lengths(frame, cell_spatial) ;
cell_lengths:units = "angstrom" ;
double cell_angles(frame, cell_angular) ;
cell_angles:units = "degree" ;
// global attributes:
:title = "" ;
:application = "AMBER" ;
:program = "sander" ;
:programVersion = "9.0" ;
:Conventions = "AMBER" ;
:ConventionVersion = "1.0" ;
data:
spatial = "" ;
time = 4079, 4080,
Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
SB - ISIC - LCBC
BCH 4108
CH - 1015 Lausanne
On Aug 24, 2007, at 3:03 PM, Chris Moth wrote:
> 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 Wed Aug 29 2007 - 06:07:17 PDT
