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Some lectures and job postings are now available. See upload log for update history and giving for donation. Contact info is given below.
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 solvation 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.

Online visualization is working now!

Please note 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 by using the provided inputs.
  • A protein dielectric constant is set to 1, but a user can adjust it if necessary.
  • The OPM PDB does not contain "TER" between ATOM and HETATM, so that CHARMM-GUI often fails to recognize ligand molecules. In such case, the user should manually insert "TER" in appropriate places.
References for PBEQ Solver:

S. Jo, T. Kim, V.G. Iyer, and W. Im (2008)
CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865

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

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