[apbs-users] Electrostatic Energy for Each Atom

[Fernando Bruno]

Hi all, 

I calculate the electrostatic energy components for each atom by APBS, because my focus is researching which atoms does not stabilize the protein that I work. So, I found some works which electrostatic energy was calculated by other methods, as TKSA, but I coudn't find results obtained by APBS. 

My question is: (1) Is it possible to perform this analysis by APBS?

                         (2) Does somebody knows some  work with this focus?

Could someone help me with this?

Best wishes,

--

Fernando Bruno da Silva

Master's Program: Molecular Biophysics

Graduate: Physics

Instituto de Biociências, Letras e Ciências Exatas

UNESP - Campus São José do Rio Preto

_______CONTACT INFORMATION________

Phone: +55 (17) 99658-5684

Secretary: +55 (17) 3221-2240

Skype: fern.brun

http://calvin.df.ibilce.unesp.br/

[Nathan Baker]

Hello --

You can use the "write atompot" ELEC command (http://www.poissonboltzmann.org/docs/apbs-overview/#elec) to do this.  You will need to write out the atom potentials for two calculations:  the system of interest and a reference system (e.g., with uniform dielectric) with the same coordinates.  Subtracting the results of these calculations and multiplying by the atomic charges should give you the energies you're requesting.

Thanks,

Nathan

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From: Fernando Bruno <fernandobr...@gmail.com>
Sent: Wednesday, November 16, 2016 9:56:19 AM
To: nathanan...@gmail.com; apbs-...@lists.sourceforge.net
Subject: Electrostatic Energy for Each Atom