[Chimera-users] GROMACS trajectory

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 29 08:40:51 PDT 2009

Dear Dave,
When reporting a problem it is best to say what version of Chimera and  
what type of computer you are using.  You can use "Help... Report a  
Bug" from the Chimera menu which will automatically include this  
information in what it sends to us.

However, it is not necessary in this case since I believe the problem  
has been fixed.

I tried your files in both 1.3 (latest production release, Dec 2008)  
and the current daily build.  The production release gave the error,  
but in the daily build, MD Movie read the files successfully.   
Probably there were some cases that were not handled in the earlier  
version that have now been fixed.

Daily builds:

I recommend keeping your production release in addition to one or more  
daily builds... just give them different names or put them in  
different places.  Best,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 28, 2009, at 7:11 PM, Dave Hassan wrote:

> Hi All,
> I'm trying to generate an MD move from a gromacs trajectory. I used
> tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the
> following error message:
> VERSION 4.0.5
> using floats
> version 58  generation 17
> 9975 atoms
> 17 atoms
> 456 residues
> <type 'exceptions.IndexError'> Exception in Tk callback

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