Re: [AMBER] High PB deltaG values from MMPBSA.py calculation

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 2 Dec 2015 09:25:20 -0500

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
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