Re: [AMBER] igb=1 and gbsa=0

From: David A Case <>
Date: Tue, 8 Mar 2011 08:00:11 -0500

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.


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Received on Tue Mar 08 2011 - 05:30:02 PST
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