They are different methods that employ different approximations. GBSA
typically doesn't take into effect protein relaxation or any kind of
binding-dependent conformational changes. This will likely destabilize the
receptor slightly if you're only considering bound-state receptor
conformations, hence the lower free energy of binding with GBSA.
Hope this helps,
Jason
On Sat, Sep 18, 2010 at 3:57 PM, MEHMET ALI OZTURK <mehozturk.ku.edu.tr>wrote:
> Hi,
>
> I am investigating the binding free energy of a pentapeptide to a receptor
> with Steered MD and GBSA . For SMD I have used,
>
> "Constant velocity SMD simulation with force constant k=7 and velocity
> 0.00001 Å/ps until work graphics are converged. "
>
> For GBSA the following is done,
>
> Internal dielectric constant is taken 2 and external dielectric constant is
> 80. Bondi radii is used as 2 Ǻ for GB analysis. LCPO method is used with γ
> value taken as 0.005 and β value taken as 0 for nonpolar
> contributions.Entropy terms are calculated by NMODE module with ε = 4Ri.
>
>
>
> For SMD binding free energy is found to be -3,5 kcal/mole ; but from GBSA
> it
> is found -7,33 kcal/mol.
>
>
> Can anybody help for the reason of this difference?
>
>
> Thanks in advance,
>
> Mehmet Ali Öztürk
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Sep 18 2010 - 15:00:03 PDT
