Thank you very much!
Denis
2012/12/11 Jason Swails <jason.swails.gmail.com>
> This is because decomp and standard MM/PBSA use different methods to
> calculate the surface area. While standard MM/PBSA uses LCPO (gbsa=1) to
> calculate the surface area, decomp calculations use a method that
> recursively approximates a sphere around each atom (gbsa=2).
>
> The manual has more information on this. I am probably more inclined to
> trust the LCPO results than the other method, although your results are not
> terribly different between the two methods (~3kcal/mol difference in ESURF
> energies). Due to the (small) size of your system, it's not surprising
> that the results are as different as they are -- I would expect for larger
> systems (i.e., significantly more than 9 residues), this difference would
> be less pronounced.
>
> HTH,
> Jason
>
> On Tue, Dec 11, 2012 at 3:49 AM, Liu Denis <cndenis.gmail.com> wrote:
>
> > Dear Amber Members:
> > I used MMPBSA.py to calculate MMGBSA, the result difference whether
> I
> > use decomp or not. The output files were attached below. The difference
> > was cause by ESURF. Which result should I trust?
> > Does it the same problem with:
> > http://archive.ambermd.org/201208/0315.html ?
> > Thank you!
> >
> > Best Regard
> >
> > Denis
> > --
> > ----GnuPG Public Key----
> > Key ID: 0x488C9571
> > Fingerprint: C292 D888 D713 4D13 57F0 C07D 16F3 10C9 488C 9571
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
----GnuPG Public Key----
Key ID: 0x488C9571
Fingerprint: C292 D888 D713 4D13 57F0 C07D 16F3 10C9 488C 9571
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 11 2012 - 17:00:02 PST
