On Mon, Jul 8, 2013 at 2:32 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
> I am trying to run the fix_traj_parm.py script I got from the
> http://jswails.wikidot.com/helpful-scripts#toc21 web page. Although
> scientific python and python-netcfd are installed on my machine, I still
> get an error saying:
>
> Traceback (most recent call last):
> File "./fix_traj_parm.py", line 13, in <module>
> from chemistry.amber.readparm import AmberParm, NetCDFFile,
> open_netcdf, np
> ImportError: cannot import name open_netcdf
>
Ugh. open_netcdf never made it into update.3 for AmberTools 13 (it's only
in the local development tree). I had to add this function so that
Scientific.IO.NetCDF would have the same API as netCDF4 (since the latter
package needs to be told to create NetCDF version 3 files explicitly, yet
Scientific.IO.NetCDF does not recognize that argument).
Apparently I didn't realize this until after I had released the patch...
Since this patch is actually required for ParmEd to print out a NetCDF
restart that Amber will understand, [1] I will create a fix for this.
After applying this next update (available shortly), fix_traj_parm.py
should just work.
Thanks for pointing this out,
Jason
[1] Amber bundles NetCDF v.3, but has the ability to link external NetCDF
libraries. If you link to an external NetCDF that is new enough, then
Amber programs should recognize ParmEd-created NetCDF files just fine.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 08 2013 - 13:30:03 PDT
