> In the crystal structure, I have two K+ ions in the centre of DNA
> (quadruplex). After production run, one of the ions move out from the tetrad
> to the bulk solution and no K+ ion from the bulk solution replaces it.
>
> I guess that the K+ should be present in the tetrad as it was found in the
> crystal structure. Is the result feasible?
It's possible that in solution the K+ is much less likely to be
there. Are the K+ positions symmetrical?
You could also run more trajectories with different initial
conditions (e.g. different random number seed) to see whether
the same thing happens.
Bill
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Received on Fri May 28 2010 - 10:30:03 PDT
