AMBER: Gibbs perturb DNA strands separate

From: <>
Date: Tue, 7 Jun 2005 13:16:41 +0200 (CEST)

Dear amber users,

I am doing a perturbation with gibbs (amber7) and I mutate two hidrogen-
bonded base pairs at the same time in a DNA double helix (dickerson

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       |
|                            |
|                                                   |
|   C/ Josep Samitier 1-5    08028 Barcelona	    |
|   Tel: +34.93.403.71.55   Fax: +34.93.403.71.57   |
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Received on Tue Jun 07 2005 - 12:53:01 PDT
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