AMBER Archive (2005)

Subject: Re: AMBER: DNA strands separate

From: ivan_at_mmb.pcb.ub.es
Date: Wed Jul 06 2005 - 09:39:04 CDT

Hi,

I see ...

I think this is not the case because I have made two simulations without
perturbing for both the initial and final state of my perturbation and
they seem stable, therefore I think that the resason for my
DNA-separation is the way the perturbation is being carried out and I assume the parameters and
atomic charges are ok.

Am I right with this assumption?

Cheers,

Ivan

On Wed, 6 Jul 2005, Angelo Pugliese wrote:

> Hi Ivan,
>
> I mean may be the changed parameters could affect the stability of the helix. Of
> course I mean the parameters before the tragic event.
>
> Sorry maybe i did not explain my thoughts very clearly.
>
> Angelo
>
>
>
> ivan_at_mmb.pcb.ub.es wrote:
>
> > 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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-- 
   _______________________________________________
 /                                                 \
/   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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