On Fri, 2014-05-09 at 19:01 +0530, Arunima Shilpi wrote:
> Dear Sir
>
> I have query as to what is the significance of delta Ggas and delta Gsolv.
> I also have the query as why delta G solv is positive.
Try to rationalize your observations using the thermodynamic cycle I
mentioned in my last email. These are good questions to ask yourself
and should lead to a better understanding of the theoretical
underpinnings of MM/PBSA (which will help you better understand its
strengths and limitations).
One of the disadvantages of MM/PBSA calculations in Amber, in my
opinion, is that the calculations are easier to run than they are to
understand...
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 09 2014 - 07:00:04 PDT
