1.2. Amber/iAPBS Module

The Amber/APBS interface makes most of the APBS functionality available to Amber users. The APBS interface in sander is accessible through the &apbs keyword. Additionally, the igb keyword must be set to 6. This combination of keywords means that a calculation will be performed on a given system in vacuum and then APBS calculated solvation energies and forces will be added to the total energy and forces.

In addition to minimization and molecular dynamics simulation with APBS calculated implicit solvent contribution the Amber/APBS module can write out calculated electrostatic potential to a file. This file can be visualized using third party applications, including VMD, Pymol, PMV/Vision and OpenDX.

The current version of the Amber/APBS module supports serial execution only. Parallel capability will be added in later versions.