On Mon, Jul 9, 2012 at 7:18 AM, George Tzotzos <gtzotzos.me.com> wrote:
> I used MMPBSA.py to calculate deltaG of binding of protein-ligand complex
> after 10ns MD simulation.
>
> The result is shown in the following line
>
> DELTA G binding = -35.5263 +/- 2.7449
> 0.1228
>
> I then performed per-residue decomposition on the same trajectory and
> topology files and got the following result
>
> DELTA G binding = -37.4528 +/- 2.6611
> 0.1190
>
> The discrepancy in the Poisson Boltzmann calculation was not significant
> (see below)
>
> DELTA G binding = -29.2195 +/- 3.2998
> 0.1476
>
> DELTA G binding = -28.9779 +/- 3.2726
> 0.1464
>
> I'm using Amber11 and AmberTools 1.5
>
> Any suggestions regarding the discrepancy observed in the GB calculation
> would be most welcome
>
Check the exact place where the differences occur. The SA part of the GBSA
(the non-polar solvation) is calculated via a different method. When
decomp is turned on, the icosa method is used (recursively building
icosahedra around each atom to estimate the surface area), whereas when
decomp is turned off, the LCPO method is used.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 09 2012 - 09:00:03 PDT
