Re: [AMBER] bond distances in amber

From: Jason Swails <>
Date: Fri, 07 Nov 2014 07:55:38 -0500

On Fri, 2014-11-07 at 15:17 +0530, Mary Varughese wrote:
> Sir,
> Usually C-N bond distance is ~1.47 angstroms.
> In DNA and RNA, the A nucleotide has C-N (C1'-N9) distance given as
> 1.52 angstrom (from leap). if in a struture this distance is 1.45
> angstrom. does amber force it to 1.52 and would it cause any
> instabilty to the system? is this distance difference significant?

Let's have a look. The C1' and N9 atom types in the 'A' residue of
nucleic12.lib have atom types CT and N*. If we look at parm10.dat where
those parameters are defined, we see the line:

CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA

showing that the equilibrium bond distance is 1.475 Ang and the bond
force constant is 337.0 kcal/mol/A^2 (this is actually half of the force
constant defined by Hooke's law, so the "canonical" force constant is
actually 674.0 kcal/mol/A^2). So the bond potential applies a force
between those two atoms pushing or pulling their distance toward the
value of 1.475 A.

Now let's look at the Energy (E=1/2.k.(x-x0)^2) and the force
(F=-k(x-x0)). At a distance of 1.47 A as you asked, the bond energy
here becomes 0.0084 kcal/mol with a force of 3.37 kcal/mol/A. If we
instead look at the distance 1.52, we see that our bond energy is 0.682
kcal/mol and our force is 30.33 kcal/mol/A.

This energy is reasonably small -- on the order of kT. I look at
energies because forces are harder to gauge whether they are "big" or
"small", since we don't commonly think in terms of forces when doing
biochemistry. You can run some other back-of-the-envelope calculations
(like the electrostatic force between two monovalent ions separated by
10 Angstroms) to get a general idea of how "big" 30.33 kcal/mol/A is
compared to other forces arising in the force field.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 07 2014 - 05:00:03 PST
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