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
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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 Tue Dec 11 2012 - 05:30:02 PST
