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