Thanks Dears Ilyas and Francesco!
I write a code in c++ to extract base stacking information,but I don't know it's precision.
Dear Francesco, I'll be Happy if you send me that source code.
I want to compare my c++ code with that.
Best Regards,
Amir
> 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 Thu Mar 08 2012 - 11:30:04 PST
