AMBER Archive (2007)

Subject: AMBER: amber md movie using Chimera

From: Wang, Xuelin (Xuelin.Wang_at_stjude.org)
Date: Wed Sep 05 2007 - 12:42:08 CDT

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

 

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