[Chimera-users] (no subject)

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 5 11:24:03 PDT 2007

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:



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

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