On Wed, Dec 2, 2015 at 8:59 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am working with a dimeric protein system and I am trying to calculate
> the binding free energy change between two monomeric units in presence and
> absence of bound ligand, using MMPBSA.py. Though the calculation finished
> successfully, I find a huge difference between the GB and PB deltaG values
> for the same system.
>
> In presnce of ligand, the GB value is -67.17 and the calculate PB value
> for the same system is -675.37. Similarly, in absence of ligand, the GB
> value is -82.54 and the calculate PB value for the same system is -810.19.
>
Something seems wrong with these numbers. GB and PB should be relatively
close in general, and should certainly not differ by an order of
magnitude...
The GB results seem typical of MMPBSA results. PB does not.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 02 2015 - 06:30:09 PST
