Options pertaining to a single Poisson-Boltzman equation are located in the ELEC Window. Since APBS does not provide default values for any of the required fields, the plugin does its best to fill in appropriate numbers. More information about APBS ELEC statements can be found in the APBS Documentation. Remember that the plugin does not yet support the fields newly available in APBS 0.3.0.

Calculation Type

The Calculation menu includes the list of calculation types that APBS can perform. The fields listed in the window are changed when a different calculation type is selected. This menu also allows the user to choose whether a linear or nonlinear equation is used.

Molecule Selection

Any molecule loaded in VMD can be used for a calculation. A VMD atom selection can be used, e.g., to remove waters before running APBS.

Output Menu

The Output menu presents a list of the maps that can be created by APBS. Any combination of maps can be selected in the menu.

Grid Centers

Grid centers can be specified using either a molecule or coordinates. Any molecule loaded in VMD can be selected, and the grid will be centered at the center of the molecule.