Since you stripped water and ions from the trajecotry file, you need a
new topology without those molecules to match the new traj file.
On Wed, 2007-09-05 at 12:42 -0500, Wang, Xuelin wrote:
> Dear amber 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?
>
>
>
> Thanks
>
> Xuelin
>
>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 09 2007 - 06:07:09 PDT
