Just add a bit to Jason' reply.
We have updated new nucleic acid parameters for igb8 in Ambertools 15, (have better performance.)
But try with PB calculation first. Try with GB later if speed is important.
Hai
> On Mar 11, 2016, at 7:51 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 - 17:30:04 PST
