Input Generator

• PDB Reader
• Solvator
• Quick MD Simulator
• Membrane Builder
• Boundary Potential Utilizer
• PBEQ Solver
• Implicit Solvent Modeller
• Normal Mode Analyzer
• NMR Structure Calculator
• User Space

PBEQ Solver

The PBEQ Solver calculates and visualizes the electrostatic potential of your molecule by solving the Poisson-Boltzmann (PB) equation. This module allows you to calculate

• Electrostatic potential and solvantion energy ,
• Protein-protein electrostatic interaction energy , and
• pKa of a titratible residue

in both aqueous solvent and membrane environments. Users can specify various physical parameters for PB calculations and interactively visualize the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours.

It should be noted that all the calculations are performed with coarse grid spacing (1.5 Angstrom before and 1 Angstrom after focusing) for efficient calculation and visualization. It is recommended to use 1 ~ 1.5 Angstrom before and at least 0.5 Angstrom after focusing in practical applications.

Reference:

W. Im, D. Beglov, and B. Roux (1998)
Continuum Solvation Model: Computation of Electrostatic Forces from Numerical Solutions to the Poisson-Boltzmann Equation. Comput. Phys. Comm. 111:59-75

S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im (2008)
PBEQ-Solver for Online Visualization of Electrostatic Potential of Biomolecules. Nucl. Acids Res. 36:W270-275