On Tue, Oct 2, 2012 at 5:00 AM, setyanto md <stwahyudi.md.gmail.com> wrote:
> Dear Amber User and Developer,
>
> I should say sorry if this questions happened many times.
>
> 1. What is the Different between PBSA and MMPBSA, I've read in
> AmbertTools12 there was chapter for PBSA and MMPBSA.
>
PBSA is a program for calculating the solvation free energy of a
(macro)molecule according to the Poisson-Boltzmann equation. MM/PBSA is a
script that automates the procedure of carrying out end-state free energy
calculations. MM/PBSA can also be thought of as a program that simplifies
the procedure of calculating PB and GB (and others, like 3D-RISM) solvation
free energies for an ensemble of snapshots. So MMPBSA provides a reduced
set of parameters to tune PB calculations (a simplistic interface to PBSA).
2. I'd like to calculate solvation energy, which one shoul I used: PBSA or
> MMPBSA ?
>
If you need more functionality than MMPBSA has to offer (check the manual),
then use PBSA. Otherwise, it may be easier to use MM/PBSA. Although it's
important to understand what is being done. The manual points to good
resources (and the manuscript for MMPBSA.py is here:
http://pubs.acs.org/doi/abs/10.1021/ct300418h
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 02 2012 - 05:00:02 PDT
