Re: [AMBER] problems

From: Jason Swails <>
Date: Mon, 8 Jul 2013 16:21:06 -0400

On Mon, Jul 8, 2013 at 2:32 PM, Fabrício Bracht <> wrote:

> I am trying to run the script I got from the
> 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 "./", 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),
should just work.

Thanks for pointing this out,

[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
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Received on Mon Jul 08 2013 - 13:30:03 PDT
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