A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods

This work introduces a continuous smooth permittivity function into Poisson–Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins. The permittivity function is derived using a Gaussian method to describe volume exclusion. The new method allows a rigorous determination of solvent forces within a grid-based technology. The generality of approach is demonstrated by considering a range of applications for small molecules and macromolecules. We also present a very complete statistical analysis of grid errors, and show that the accuracy of our Gaussian-based method is improved over standard techniques. The method has been implemented in a new code called ZAP, which is freely available to academic institutions.1 © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 608–640, 2001