AMBER Archive (2006)

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

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Sun Apr 23 2006 - 23:13:30 CDT

Thank you for your particular explanation. I learned a lot from your reply.

Best Wishes,
Chengwen

On 4/22/06, Michael Crowley <crowley_at_scripps.edu> wrote:
>
> 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.
> Mike
>
> 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
> 10550 North Torrey Pines Road
> La Jolla, California 92037
>
> Electronic mail: crowley_at_scripps.edu
> Telephone: 858/784-9290
> Fax: 858/784-8688
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