Dear Jason,
Thanks for the reply.
Do you know why this link cannot be accesed :
http://amber.scripps.edu/tutorial/shirts/index.html ?
regards
setyanto
On Tue, Oct 2, 2012 at 6:31 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 05:00:03 PDT
