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.mmb.pcb.ub.es |
| theochem.hotmail.com |
| Website: http://mmb.pcb.ub.es/~ivan |
\ /
\_________________________________________________/
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Received on Wed Jul 06 2005 - 11:53:01 PDT
