Re: [AMBER] Keeping an hexamer whole.

From: Jason Swails <>
Date: Wed, 4 Dec 2013 20:56:13 -0500

On Wed, Dec 4, 2013 at 7:38 PM, Julio Dominguez <>wrote:

> Dear amberists,
> We are simulating a hexamer with six ligands but we are unable to make a
> "movie" of the complex in the proper oligomeric form. That is, we have fail
> in our attempts at centering all the subunits and ligands.
> We have use the autoimage, center and image commands in various
> combinations (within cpptraj):

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

In cases like this, I tend to use autoimage to start, then a combination of
"center" and "image" commands. So something like this (assuming the
hexamer is residues 1 to 1602 and the ligands are residues 1603 to 1608):

center :1-1602 mass origin
image origin center [familiar]

Familiar is necessary if you do not have an orthorhombic cell (something
like a truncated octahedron, for instance). The "familiar" keyword will
transform the general triclinic cell into its most spherically symmetric
representation. The above commands will work great if each monomer in the
hexamer is large and the ligands are small.

An alternative if the above does not work (which is possible if the hexamer
is large compared to the size of the box but each monomer is small) is to
center each monomer one at a time and then image everything at the end, so
something like this:

center :1-267 mass origin
image origin center [familiar]
center :1-801 mass origin
image origin center [familiar]
center :1-1602 mass origin
image origin center [familiar]

(You can use more center and image commands and center one more monomer
each time if the above still does not work). It may require some

Good luck,

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.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 04 2013 - 18:00:03 PST
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