Re: [AMBER] Base stacking

From: amirhossein taghavi <amirhosseintaghavi786.hotmail.com>
Date: Fri, 9 Mar 2012 15:33:51 +0000

Hi,

I somehow agree with Ilyas can someone give a definition for base stacking ... as I have done some QM studies on base stability, papers mostly agree that the stabilization of base stacking
involves London dispersion forces and interactions
between partial charges within the adjacent rings but as these interactions are not characterized and parameterized instead the geometrical approach by prof Prevost (J. Mol. Graphics, 14:6-11, 1996) is usually used.
prof Hobza have done a through qm calculation on base stacking that might be so helpful to look at (J. Am. Chem. Soc., 2002, 124 (39), pp 1180211808).
I do not believe that merely geometrical approaches could be defined as base stacking!!

Regards
 

> Date: Thu, 8 Mar 2012 20:00:49 +0100
> From: francesco.oteri.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Base stacking
>
> Hi Amir,
> I solved the problem in http://dx.doi.org/10.1021/jp203999x where I
> calculated stacking features.
>
> Basically, is have written a gromacs program that calculates for each
> base-plane the geometric center and the normal to the plane.
>
> The software analyzes your nucleic acid frame by frame and detects a
> stacking if the geometric center between any base pair is smaller than a
> cut-off (default 5Angstrom)
> and if the angle between the two planes is between 0 and 30 (this value can
> be also changed).
> If the requirements fit your needs, I can send you the source code.
>
> Francesco
>
>
>
> Il giorno 08 marzo 2012 19:39, Ilyas Yildirim
> <i-yildirim.northwestern.edu>ha scritto:
>
> > You cannot find such a number because how will you define a
> > "base-stacking"? You better calculate the overlap areas of the bases with
> > respect to time using X3DNA. Overlap areas of the bases will tell you how
> > stacking is (strong or weak).
> >
> > Ilyas Yildirim, Ph.D.
> > -----------------------------------------------------------
> > = Department of Chemistry - 2145 Sheridan Road =
> > = Northwestern University - Evanston, IL 60208 =
> > = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > -----------------------------------------------------------
> >
> > On Thu, 8 Mar 2012, amir abbasi wrote:
> >
> > >
> > > I meant number of base-stackings trough trajectory.
> > > In the other words how many base-stacking do I have?
> > >
> > >> From: amirhosseintaghavi786.hotmail.com
> > >> To: amber.ambermd.org
> > >> Date: Thu, 8 Mar 2012 17:18:27 +0000
> > >> Subject: Re: [AMBER] Base stacking
> > >>
> > >>
> > >> Hi,
> > >>
> > >> would you please be more precise..what do you mean by base stacking
> > number??
> > >>
> > >>
> > >>
> > >>> From: amir-abbasi.hotmail.com
> > >>> To: amber.ambermd.org
> > >>> Date: Thu, 8 Mar 2012 14:43:51 +0330
> > >>> Subject: [AMBER] Base stacking
> > >>>
> > >>>
> > >>> Hi!
> > >>> I want to extract base stacking number from mdcrd file.
> > >>> Is there any analyzing program to do this or not?
> > >>> Best regards,
> > >>> Amir
> > >>>
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
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Received on Fri Mar 09 2012 - 08:00:03 PST
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