AMBER Archive (2003)

Subject: Re: AMBER: how to measure the minor groove widths of a DNA?

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Oct 29 2003 - 11:31:09 CST

> I am running a testing job for a DNA in water. I want to compare my
> results with a literature figure about the minor groove widths along the
> base pairs, can any one give me some hint on what to measure ? (I am going
> to use Carnal)
>
> I am not a bio people and new to the AMBER.

It would be very wise to consult the literature on this; you should become
a "bio" person if you want to do simulations of biomolecules. Often
running the program is the easy part; figuring out what the simulation
results mean is where it gets tricky. There is a vast literature on
analyzing DNA structure/properties.

First step is to see what values you are comparing to. If you are
comparing specifically to someone else's published work, see how they
defined the minor groove width. There are many variations in the
literature. You can choose close phosphate-phosphate distances (+/- the
phosphate radii), you can spline fit a function to the groove and measure
across this (as is done in Curves), etc., etc. The easiest way is
measuring P-P distances. If you are comparing to a crystal structure, the
close approach P-P distances may be reasonable if you measure consistently
between your simulation and the crystal.

Good luck,

\ 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
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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