Hi Jason. Sorry to bother you so soon, but, just so that I can program
myself, you said that an update would be available shortly. Any idea when
that shortly is going to be? Again, sorry to bother you with this.
Thank you
Fabrício
2013/7/8 Jason Swails <jason.swails.gmail.com>
> 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 Thu Jul 11 2013 - 10:00:03 PDT
