# Re: [AMBER] bond distances in amber

From: Mary Varughese <maryvj1985.gmail.com>
Date: Sat, 8 Nov 2014 22:45:21 +0530

Sir,

I got some valuable information. i am really thankful for the reply.
sir, if the parm10.dat provides C1'-N9 equillibrium distance as 1.475
angstrom why 1.52 angstrom in the pdb file i saved from xleap with ff10

On Fri, Nov 7, 2014 at 6:25 PM, Jason Swails <jason.swails.gmail.com> wrote:

> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Sat Nov 08 2014 - 09:30:02 PST
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