Re: AMBER: distance between images

From: Thomas E. Cheatham, III <>
Date: Thu, 14 Oct 2004 09:51:33 -0600 (Mountain Daylight Time)

> is there any routine to calculate the minimum distance between two images of
> the solute during an MD trajectory? I'm using a truncated octahedron box, and
> would like to check whether the protein in the box is interacting with its
> image(s).

ptraj will do this automatically with the distance command (i.e. report
the shortest "imaged" distance unless the "noimage" keyword is specified.
This works for calculating a specific/single distance (between atoms or
center of masses of groups of atoms).

This doesn't easily help you determine if the two images are interacting
since if the molecule is rotating you do not know which parts may

The hbond facility may be a more general (but expensive) way of
determining it, however at present (without a minor code modification in
the call to calculateDistance2 in transformHBond in actions.c), it
does not calculate the minimum image distance.

An alternative method is to use the image command to shift
to adjacent boxes/unit cells; i.e. you could build a set of PDB files
of the original structure plus its shifted images +/- 1.0 unit cells and
then view all of these...

        trajin mdcrd
        center .CA mass origin
        image origin center xoffset 1 yoffset 0 zoffset 0
         average pdb avg_x1y0z0.pdb .CA

then run again with xoffset -1, yoffset = 0, etc. and all possible
combinations (running ptraj for each separate input). This can provide a
means of "seeing" all the interactions by viewing all the pdbs. [A future
modification to trajout may be to allow dumping multiple images

\ 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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Received on Thu Oct 14 2004 - 16:53:00 PDT
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