Do you use the Glycam force field for any part of the simulation, by any
chance?
On Mon, Jul 9, 2012 at 1:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thanks Jason,
>
> The difference is in EGB
>
>
> The question is which of the two results is more reliable? The calculation
> with or without the LCPO method?
>
> EGB 15.6232 3.4347
> 0.1536 (per-residue decomposition)
> EGB 17.3176 3.5050
> 0.1567 (no decomposition)
>
> I know that these energies are relative, but for comparison purposes it'd
> be good to know.
>
> Best regards
>
> George
>
>
> On Jul 9, 2012, at 5:50 PM, Jason Swails wrote:
>
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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--
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 - 13:30:02 PDT
