On Fri, Mar 11, 2016 at 6:09 PM, Arati Paudyal <apsilwal123.gmail.com>
wrote:
> Dear all,
>
> While running GBSA to calcualte free energy change of a protein complex, I
> am kind of confused on what I should be using for "igb". I looked at the
> manual and that was too "algorithmic" explanation for beginner user like me
> to understand. So, could you please suggest what "igb" value should I use
> for my purpose? I have a protein complex and I want to find the Delta G
> using PB/GBSA.
>
For proteins and nucleic acids, igb=8 typically performs the best.
>
> Also, what salt concentration do we pick for the salt conc? My guess is
> that we use similar salt concentration to that of experimental condition.
> Is this right??
>
Yes. For large salt concentrations, the simple model used in the GB code
is a much poorer approximation, though (we're talking concentrations around
.5M and greater, I think).
HTH,
Jason
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Received on Fri Mar 11 2016 - 17:00:05 PST
