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
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Received on Thu May 31 2012 - 11:00:02 PDT
