Re: [AMBER] Problem with visualization in VMD after using AUTOIMAGE

From: Daniel Roe <>
Date: Thu, 11 Jul 2013 11:38:23 -0600


In the future I recommend you send these questions to the entire Amber
mailing list. This may help other people who may encounter similar
issues in the future:

On Thu, Jul 11, 2013 at 10:15 AM, Nupur Bansal <> wrote:
> My protein is a dimeric protein and when I visualized it in VMD, it appeared as if it split into two subunits.
> To solve this rendering issue, I used AUTOIMAGE and processed the trajectory. But after doing that, I am unable to load the trajectory in VMD.

You'll have to provide more information. What was your exact input to
cpptraj? Did you write your trajectory in the same format it was read
in? Did you perform any stripping of atoms or removal of box
coordinates that would cause the output trajectory to no longer match
up with the original topology?


> Can you help me with this?
> Thanks
> Nupur

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Jul 11 2013 - 11:00:03 PDT
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