AMBER Archive (2005)

Subject: Re: AMBER: DNA strands separate

From: ivan_at_mmb.pcb.ub.es
Date: Wed Jul 06 2005 - 08:40:18 CDT

Dear Angelo,

Sorry, I don't exactly see what you mean

In my perturbation the DNA double helix is completely destroyed and
therefore I can't measure any parameter with Curves. My two modifications
surely will change these parameters but the DNA double helix should keep
its normal appeareance.

Did I understand your suggestion properly?

thanks a lot,

Ivan

On Wed, 6 Jul 2005, Angelo Pugliese wrote:

> HI Ivan,
>
> Did u check if your two modifications changed the parameters of the double
> helix.....i mean over all the lenght of the double helix? U can use a program
> like CURVES to measure these parameters.
>
> Angelo
>
>
> ivan_at_mmb.pcb.ub.es wrote:
>
> > Dear amber users,
> >
> > I am doing a perturbation (MD/TI) with sander (amber8) and I mutate two
> > hidrogen- bonded base pairs at the same time in a DNA double helix (dickerson
> > dodecamer).
> >
> > My mutation consists in Ade --> Gua, and Cyto1 --> Cyto2 ( where cytoX
> > are two tautomers of cytosine)
> >
> > I made a prior equilibration of the system and nothing anomalous happens,
> > but when I turn to the perturbation I found that the DNA strands separate
> > along the perturbation i.e. firstly, some hidrogen bonds increase their
> > distance and finally the whole helix is completely open.
> >
> > I would think that this could be because of two appearing/disappearing
> > groups that leads to an instability but this would also mean that the
> > DNA separation would begin in the base pairs that I am mutating, and this
> > is not my case.
> >
> > What reason can a DNA double helix have to get separated ? I guess that
> > this can be due to some kind of erronous electrostatic interactions but I
> > have carefully checked my charges ...
> >
> > Please, any comments are kindly acknowledged.
> >
> > thanks in advance
> >
> > --
> > _______________________________________________
> > / \
> > / Ivan Marchan Carvajal \
> > | (PhD Student) |
> > | |
> > | Institut de Recerca Biomedica de Barcelona |
> > | Parc Cientific de Barcelona |
> > | Molecular Modelling & Bionformatics Group |
> > | http://mmb.pcb.ub.es |
> > | |
> > | C/ Josep Samitier 1-5 08028 Barcelona |
> > | Tel: +34.93.403.71.55 Fax: +34.93.403.71.57 |
> > | |
> > | E-mail: ivan_at_mmb.pcb.ub.es |
> > | theochem_at_hotmail.com |
> > | Website: http://mmb.pcb.ub.es/~ivan |
> > \ /
> > \_________________________________________________/
> >
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