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 - 11:30:02 PST
