APBS Setup widget

Open APBS Setup widget: Compute → Electrostatics → Setup.

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.

When Calculate type is set to Solvation energy, APBS calculates total energy of a molecule twice, once in a solvent (E_solvent) and once in a vacuum (E_vacuum). The Solvation energy is outputted as E_solvent - E_vacuum. 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.