AMBER Archive (2005)

Subject: Re: AMBER: DNA strands separate

From: Angelo Pugliese (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Wed Jul 06 2005 - 07:46:05 CDT

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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