AMBER Archive (2004)

Subject: Re: AMBER: An question about PTRAJ

From: Thomas E. Cheatham, III (
Date: Sat Sep 11 2004 - 14:06:05 CDT

> together. According the instruction, I use the IMAGE. But I can't solve the
> problem.
> The commands which I had used are listed bleow:
> 1, image origin, I got single strand back. The other one is still in the other
> side of the box.
> 2, image center bymask :195-218, no function.
> 3, image center:195-218 bymask :195-218, still no function
> the 195-218 is the residue number of DNA double helix

It is a little confusing at first to understand what is happening, however
you want to think about is a combination of operations that include
centering the molecules and then imaging them.

Imaging simply moves molecules "outside the box" back into it. It's frame
of reference is the origin (0,0,0) or the box center (depending on whether
you specify the origin keyword). I normally center/image to the origin.

If two molecules are separated, if you center to the origin, the center of
mass of the two molecules may both be within the box yet the molecules are
separated. To remedy this, center one of the molecules first, and image

So, let's assume your protein is residues 1-194 and DNA is 195-218. The
DNA is smaller so I would center and image this first.

  center :195-218 mass origin
  image origin center

This should bring the protein and DNA together (assuming sufficient

Then I would center all the solute and image again

  center :1-218 mass origin
  image origin center

The image bymask, byres etc only image part of the system; it is better
just to let everything move/image.

Also, if you are using a truncated octahedron, then it is useful to add
the familiar keyword.

  image origin center familiar

Let me or the list know if you have further questions!


\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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