[Chimera-users] Chimera doesn't display AMBER molecular dynamics trajectories with periodic boundary condition.

Eric Pettersen pett at cgl.ucsf.edu
Tue Jan 16 12:46:56 PST 2007

On a related note, there _is_ an error in the way Chimera handles  
NAMD/CHARMm DCD files _without_ periodic box information in the  
1.2304-1.2318 releases.  You will get a "DCD format error 9".  If  
this bites you, send me mail and I'll send you a file with the fix  
that you can drop into your Chimera.


On Jan 11, 2007, at 12:26 AM, juyong Lee wrote:

> Hi, I'm using chimera 1.2309 version.
> And I found out that MD movie module in chimera doesn't display  
> AMBER trajectory file with periodic condition correctly.
> I works well only with non-periodic condition trajectory file.
> Another visualization program, VMD, has two seperated options for  
> AMBER trajectory file: with periodic condition and not.
> I prefer display style of chimera. So, I really hope to see my  
> AMBER trajectory with Chimera.
> Do you have any tips for this problem? or have plan to add the  
> format, with periodic boundary condition. :-)
> Thanks again for your great program and have a nice day!
> =============================================
> Lee, juyong
> Ph.D student, Department of chemistry, Seoul National University,  
> Korea.
> drfaust23 at gmail.com
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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