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.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 20 2009 - 16:13:53 PDT
