AMBER Archive (2005)

Subject: AMBER: DNA strands separate

From: ivan_at_mmb.pcb.ub.es
Date: Wed Jul 06 2005 - 05:39:24 CDT

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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