**PBEQ**

Continuum electrostatics, in which thesolvent is represented
as a featureless dielectric medium, is an increasingly popular
approach to describe solvation of polar molecules. The approximation
goes back to Born (1920), Kirkwood (1934), and Onsager
(1936). Continuum electrostatic approximations are based upon
the Poisson Boltzmann equation for macroscopic media. The
approach is of particular interest for incorporating solvent
effects implicitly in atomic models of biomolecules. Numerical
solutions of the PB equation based on finite-difference can
be obtained routinely in the case of molecules of arbitrary
irregular shapes.

One of the most important aspect of PB calculations is the atomic
radii used to define the location of the solvent-protein dielectric
boundary. We have determine a set of atomic Born radii for
all 20 amino acids using MD/FES simulations with explicit
water molecules (Nina et al, 1997).

In most practical applications, the PB equation is solved numerically
for a fixed conformation of the biomolecular to obtain the
electrostatic solvation free energy, shifts in pKa for specific
residues, and protein-protein interactions in solution. The
electrostatic solvation forces (i.e., the first derivatives
of the solvation free energy with respect to the atomic coordinates
of the solute), can also be calculated to implement energy
minimization and dynamical algorithms. Lastly, the influence
of the transmembrane potential can be incorporated into the
theory easily using a modified form of the PB equation.
**Download:**

- Set of atomic Born radii for the 20 standard amino acids
- Complete set of atomic Born radii for proteins and nucleic acids
- Calculate the electrostatic solvation free energy
- Calculate a pKa shift
- Calculate protein-protein binding
- Calculate the transmembrane potential across the KcsA K+ channel
- Simulation with analytical electrostatic solvation forces