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APBS Setup widget

How-to change parameters.


Covers Computation and Visualization of Electrostatic Potential.
Page 3 of 4.

Open APBS Setup widget: ComputeElectrostaticsSetup.

There are following four tabs in this widget:
  1. Calculation - used for setting up Calculation type,  Boundary conditions, selecting molecules, specifying the output, etc..
  2. Grid – used for setting up grid dimensions.
  3. Physics - contains protein and solvent dielectric constant, etc.
  4. Web Services - used for running APBS remotely.
The widget opens with Calculation tab selected; where one of the most important option to select is the Calculation type. By default, Calculation type is set to Electrostatic potential, which tells APBS to calculate electrostatic potential for selected molecule. Two other options for Calculation type are Solvation energy and Binding energy.

When Calculate type is set to Solvation energy, APBS calculates total energy of a molecule twice, once in a solvent (Esolvent) and once in a vacuum (Evacuum). The Solvation energy is outputted as Esolvent - Evacuum. User can also choose to calculate binding energy between two molecules by setting Calculation type to Binding energy, in which case s/he should provide Molecule1, Molecule2 and the Complex between these two molecules. APBS then calculates the energy for Molecule1 (E1), Molecule2 (E2) and Complex (E3), and outputs the binding energy as E3 - E2- E1.

 Before finishing, have a look at the parameters in the Physics tab that can be changed as needed.

by Sargis Dallakyan last modified 2006-11-04 13:17
Contributors: Ruth Huey, Michel Sanner
Molecular Graphics Laboratory, TSRI

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