Re: [AMBER] Delta G pb and Delta G Sa

From: Wesley Michael Botello-Smith <>
Date: Mon, 3 Dec 2018 10:19:41 -0800

You don't necessarily need to use sander. If you are just interested in
processing particular frames / structures then the pbsa command can give
you this in its output (see chapter 6 of the manual). You can certainly go
through sander as well though, both can provide post processing. If you
only have a single crystal structure, you can easily do everything by hand.
MMPBSA or MMGBSA is your other option, though it may be overkill for a
single structure.

In the case of using PBSA directly you would use inp=1 if you want to
utilize the linear molecular surface area based non-polar model.
Alternativley, you could use inp=2 if you are interested in the more
advanced cavity / dispersion model. In either case, the output file will
give you relevant energy terms showing the contributions of non-polar and
polar terms.
Depending on your options, the polar term may be further decomposed as
well. E.g. you can get separate terms to for the coulombic (vacuum
electrostatic) and reaction field / PB component.

Similarly, since you are after a deltaG you can make use of the MMPBSA
module. Most of the same options exist under MMPBSA which is essentially
automating breaking the structure / trajectory into corresponding ligand,
receptor, and complex portions then running the desired PBSA / GBSA
functions and aggregating the results.

Hope that helps.
-Dr. Wesley Botello-Smith

On Mon, Dec 3, 2018 at 8:07 AM Keiran Corbett <>

> Hello,
> I want to calculate the deltaG of the polar and non polar contributions.
> I was going to use Poisson Boltzmann and Solvent accessible surface
> calculations..
> I have had a good look through the manuel and think I need to use Sander
> and Molsurf.
> I wondered if anyone had an example tutorial or command for these (I have
> had a look in the manual and am still quite confused)
> I have a pdb file of a crystal structure of protein-ligand
> Many thanks
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Dec 03 2018 - 10:30:03 PST
Custom Search