AMBER Archive (2009)

Subject: Re: [AMBER] ptraj netcdf

From: Chris Moth (chris.moth_at_Vanderbilt.Edu)
Date: Tue May 12 2009 - 10:46:31 CDT

Your trjaectory which lacks box dimensions (which is not a problem).

That error message should be removed, and perhaps replaced a gentler
message to verify (or not) that box dimensions are there.

Here is the source code in ptraj.c

      /*
        * ARE CELL_LENGTHS PRESENT?
        */
    err = nc_inq_varid(NCInfo->ncid, "cell_angles", &NCInfo->cellAngleVID);
    if (err != NC_NOERR) fprintf(stdout, "NetCDF inquiring about cell
angle variable ID: %s", nc_strerror(err));
    err = nc_inq_varid(NCInfo->ncid, "cell_lengths", &NCInfo->cellLengthVID);
    if (err != NC_NOERR) fprintf(stdout, "NetCDF inquiring about cell
length variable ID: %s", nc_strerror(err));

    if (err == NC_NOERR) {

      isBox = 1;

      err = nc_inq_varnatts(NCInfo->ncid, NCInfo->cellAngleVID, &i);
      if ( i > 0 ) {
   err = nc_inq_attlen(NCInfo->ncid, NCInfo->cellAngleVID, "units", &ist);
   if (err == NC_NOERR) {
     NCInfo->cellAngleUnits = (char *) safe_malloc(sizeof(char) * (ist+1));
     err = nc_get_att_text(NCInfo->ncid, NCInfo->cellAngleVID, "units",
NCInfo->cellAngleUnits);
   }

> Friends,
>
> While i was trying to read netcdf trajectory and write only a part of the
> trajectory with ptraj, i got the following message. Someone please write
> me
> what this means. Can i ignore this message.
>
> Checking coordinates: bound_prot.ncdf
> NetCDF inquiring about cell angle variable ID: NetCDF: Variable not
> foundNetCDF inquiring about cell length variable ID: NetCDF: Variable not
> found
>
> My input file,
> *ptraj bound.top << eof
> trajin bound_prot.ncdf 1 6037
> trajout bound.ncdf
> eof*
>
> Thanks,
> Bala
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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