[Chimera-users] gromacs trajectory - only atoms, no bonds

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 16 11:18:34 PDT 2007

	The .tpr file format is basically undocumented, so it's possible  
that I've done something wrong somewhere in my code that reads it.   
Nonetheless, every trajectory I have access to works correctly (bonds  
show up).  Could you send me your .tpr file?  It would also be nice  
if you could send a corresponding .trr file with a frame or two of  
your trajectory so I can verify that everything looks okay when I'm  
done, but it's not strictly necessary if it's hard for you to make one.
	It has been suggested that I support allowing the use of .gro files  
instead of .tpr files.  WIth a .gro file I would have to guesstimate  
connectivity and chemical elements, but in some cases (possibly this  
one for instance) it may be preferable.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Apr 16, 2007, at 1:29 AM, Moo Cow wrote:

> I believe one has to have a very recent chimera in order
> to be able to read gromacs trajectories.
> I have "beta version 1 build 2376 2007/04/11
> It is terrific that chimera can read the trajectories
> (without problem), but it then does not seem to join
> the atoms with bonds (it certainly does so for normal
> pdb files). My trajectory is displayed as a set of
> lonely unbonded atoms.
> I believe I checked for obvious mistakes on my part. I
> went to the tutorial, found the lines
>   repr stick
> and so on. They gave no error message, but did not help.
> Many thanks for any advice.
> =
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