Re: [AMBER] Keeping an hexamer whole.

From: Daniel Roe <>
Date: Wed, 4 Dec 2013 21:27:42 -0700


On Wed, Dec 4, 2013 at 6:56 PM, Jason Swails <> wrote:

> Sometimes autoimage doesn't _quite_ do what you want it to. This is
> usually the case only when you have multiple 'large' molecules (i.e.,
> non-covalently bound chains, like DNA/RNA duplexes, unbound hexameric
> proteins, etc.). The reason it doesn't always work the best is that it
> centers (anchors) the first or largest molecule and images everything
> else around it. For large systems, this may yield a periodic cell that is
> not centered around the solute of interest, but rather only a part of the
> solute.

> P.S. I think if you find out which monomer of the hexamer is supposed to be
> in the 'center', you can specify that one as your 'anchor' in the autoimage
> command. Again, experimentation is your best bet.

Just to add to this, you can specify which molecule is the "anchor"
molecule by using 'anchor <mask>'. It's best to use a molecule that has the
shortest cumulative distance to all other molecules in your system. I'll
try to give an example, pardon the crude ASCII art. Say you have a tetramer
where each monomer is named A, B, C, and D, and they are in a configuration
that looks like:


By default cpptraj chooses the first molecule (in this case monomer A) as
the anchor. In this case that would not be ideal, especially if the box
isn't very large; you'll get better results by using monomer B as the
anchor. So in your case you can try choosing a monomer that is more
"central" as your anchor and see if that improves results.

Hope this helps,


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) 585-6208 (Fax)
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Received on Wed Dec 04 2013 - 20:30:02 PST
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