AMBER Archive (2006)

Subject: Re: AMBER: a question about "solvateoct" in AMBER 8

From: Michael Crowley (
Date: Fri Apr 21 2006 - 14:50:52 CDT

Amber treats all periodic cells as triclinic. Any space-filling shape can be
recast as a triclinic cell. The correct triclinic cell for a truncated
octahedron has major crystal axes going out the diagonal faces, the ones
shaled like hexagons, not the ones shaped like diamonds/squares of the
truncated octahedron shape. If one is thinking of constructing the shape by
cutting the corners off a cube, the major directions are from the center of
the cube toward the corner of the cube. Thus the unit cell directions are 109
degrees apart and have distance of half of the diagonal across the cube:
(cube edge dist) * sqrt(3) / 2 = 73.15 * 1.73 / 2 = 63.35
Leap does add on a little for avoiding bad vdw contacts across the periodic
boundaries so you get the 64 number.

Since the question has arisen here is a little more detail:
The orientation of unit cells in amber is now required (for sander) to have
one crystal axis along the x-axis, a second in the x-y plane, and the third
wherever it ends up, I think it is always in the positive z half of space.
Thus you will see that your truncated octahedron shape is oriented by leap to
have one set of parallel hexagonal faces normal to and intersected in the
middle by the x axis. This feature might be disconcerting to someone who is
expecting to see the classic TO shape oriented as if the cube it came from
were oriented with its axes parallel to the coordinate axes.

I hope that helps, cutting to the chase, your output looks fine.

On Friday 21 April 2006 11:48, Bill Ross wrote:
> > I found out that the box size information listed in XLEAP after add the
> > solvent is different with that in ".inpcrd" file.
> >
> > solvateoct a TIP3PBOX 10.0
> >Scaling up box by a factor of 1.371926 to meet diagonal cut criterion
> > Solute vdw bounding box: 34.115 45.712 32.074
> > Total bounding box for atom centers: 73.150 73.150 73.150
> >
> > Last line in ".inpcrd" file:
> > 64.2159170 64.2159170 64.2159170 109.4712190 109.4712190 109.4712190
> The boxes reported in the execution of the cmd are for an enclosing
> rectilinear box, while the dimensions of the final inpcrd octo box
> with 109-degree angles are probably the distances between the faces
> created by chopping off the corners of the rectangular box.
> Bill
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Physical mail:   Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
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