Re: [AMBER] autoimage problem

From: David A Case <>
Date: Wed, 16 May 2018 08:59:17 -0400

On Mon, May 14, 2018, Ming Tang wrote:
> I am simulating a protein with a gold nanoparticle in an octahedral
> water box. During the simulation, the gold nanoparticle was fixed, but
> still was "separated" when I visualize the trajectory in chimera. I
> tried to use autoimage in cpptraj, but failed to fix the peridic
> issue. I tried to use fixed and origin command, but failed again. Could
> you please help to give me some guidance?

This could be a place where autoimage is not smart enough to figure out
that it is the gold-nanoparticle part that you want to keep "together".
Did you try "image "WAT"? If the gold nanoparticle is not moving, only
the waters should be imaged, which sounds like what you want.

Another option would be to use autoimage with the anchor mask set to the
gold nanoparticle. (I don't think the "fixed" option is what you want

...hope this helps...I'm only a brown-belt cpptraj guru, so maybe I'm
missing something.


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Received on Wed May 16 2018 - 06:00:08 PDT
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