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

Eric Pettersen pett at cgl.ucsf.edu
Fri Jan 12 17:52:40 PST 2007

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.

Are you saying that trying to show such a trajectory gives you an  
error, or that it just doesn't look correct?  Chimera should show  
Amber periodic-boundary trajectories without problem.  Now, a  
periodic-boundary simulation may look wrong as solvent drifts out of  
the center box.  If this is the problem, you would need to use  
ptraj's "image" command to re-image the solvent into the solute box.

> Another visualization program, VMD, has two seperated options for  
> AMBER trajectory file: with periodic condition and not.

VMD can't automatically determine whether a trajectory is PBC or not,  
whereas Chimera can -- that's why VMD has separate options.

> 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. :-)

If you are actually getting an error, or if you are already re- 
imaging your solvent and things still don't look right then if you  
send me a trajectory that exhibits the problem I will investigate.


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

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