[Chimera-users] (no subject)

[Eric Pettersen]

On Sep 5, 2007, at 10:37 AM, Wang, Xuelin wrote:
> Dear Chimera’s users:
>
> I have a problem to make an Amber MD movie using Chimera. I am sure  
> I used the right Amber top file and mdcrd file, since I can use VMD  
> to display them. In my trajectory file, I already striped water and  
> counter-ions. Only box information was left with trajectory.  
> However, when I display trajectory, all trajectories were out of  
> shape. I saw the similar thing when I used VMD to display the  
> trajectory without including PBC option. I doubt that there is  
> something wrong with box information. But I don’t know how to fix  
> it. Any ideas?
Hi Xuelin,
	Chimera doesn't handle PBC information yet.  You will have to re- 
image your trajectory with ptraj, as described in the "Re-imaging the  
trajectory back into the primary box" section of this AMBER tutorial:

http://amber.scripps.edu/tutorial/polyA-polyT_New/minandmd3.html

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20070905/a4fcdfc5/attachment.html>