AMBER Archive (2009)

Subject: RE: [AMBER] amber tools reading netcdf files

From: Cojocaru,Vlad (vlad.cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Feb 24 2009 - 12:46:27 CST

See the bug fixes of amber tools 1.2

Vlad

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Chris Moth
Sent: Tue 2/24/2009 6:35 PM
To: AMBER Mailing List
Subject: Re: [AMBER] amber tools reading netcdf files
 
Clearly you have compiled ptraj with the right parameters, as you note
you can output netcdf and look at headers with ncdump.

At the surface, it would appear ptraj simply cannot open the file (see
ptraj.c source code for this error).

Is there any chance you are running ptraj from a script which is
transferring to an alternate directory, or using an alternate userid?

It would be nice if errors like this were also accompanied by OS error
reporting. You might alter ptraj.c to print the Operating System
"errno" value (see man pages for strerror/perror/errno) when opening files.

Jeremy Harris wrote:
> Hello
>
> I have a problem reading netcdf files in ptraj. Trajin does not seem to
> recognize the format, and gives me this output:
>
> PTRAJ: trajin ex.cdf
> Checking coordinates: ex.cdf
> trajin ex.cdf ignored; could not open file (ex.cdf)
>
> This seems odd because I can make netcdf files with ptraj (trajout ex.cdf
> netcdf), and ncdump will output the correct parameters for this file. Am I
> missing a library or was I during installation?
>
> Thanks in advance,
> Jeremy Harris
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

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