As far as I know, ptraj cannot read NetCDF restart files, only cpptraj can.
HTH,
Jason
On Thu, May 31, 2012 at 1:55 PM, Joshua Adelman <jla65.pitt.edu> wrote:
> I am starting to use the new netcdf restart files available in Amber 12,
> and am running into a slight problem when using ptraj. In my ptraj file, I
> have:
>
> trajin parent.restrt
> trajin seg.mdcrd
>
> To read in the coordinates from the restart file and then the trajectory
> data. This worked fine when I was using the ASCII format. However now using
> the netcdf format (ntxo=2), I get the following errors in my ptraj log:
> --------
> PTRAJ: trajin parent.restrt
> Checking coordinates: parent.restrt
> NETCDF file:
> Yikes! netcdfGetDimensionInfo on frame, error: NetCDF: Invalid dimension
> ID or name
>
> . . .
>
> PTRAJ: trajout pcoord.nc netcdf nobox
> parent.restrt: 379119632 frames.
> seg.mdcrd: 1 frames.
>
> . . .
>
> Error detected upon reading NetCDF coordinates on set 1: NetCDF:
> Start+count exceeds dimension bound 100%
> --------
>
> I would assume that the restart file should have only a single frame (The
> seg.mdcrd is also expected to have only a single frame).
>
> When I open the parent.restrt and segment.mdcrd files using the
> netcdf4-python module in python, I see that the 'coordinates' array has
> different shapes for each. For the seg.mdcrd:
>
> In [4]: f.variables['coordinates'][:].shape
> Out[4]: (1, 70366, 3)
>
> For parent.restrt:
>
> In [8]: f.variables['coordinates'][:].shape
> Out[8]: (70366, 3)
>
> I'm not sure if this makes a difference or is a possible problem. I'm a
> fairly new Amber user and am not sure if this is potentially a bug or if
> I'm doing something incorrectly. Suggestions would be most appreciated.
>
> Thanks,
> Josh
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 31 2012 - 12:30:04 PDT
