On Tue, Mar 08, 2011, Francesco Oteri wrote:
> I have to simulate a DNA structure and I'm following the tutorial
> present on AMBER website.
> In the tutorial the igb moidel is 1 (igb=1) while gbsa flag is 0 and,
> therefore, Solvent Accessible Surface term is not calculated.
> I've two question:
>
> 1) Is it correct to neglect this terms?
There is no "correct" or "incorrect". A simulation of a DNA or RNA duplex
probably won't change its surface area very much during the simulation, so
it is reasonable to ignore the non-polar term, which is rather approximate
anyway. But as with all such decisions, it should/could be checked.
...dac
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Received on Tue Mar 08 2011 - 05:30:02 PST
