The What of Zap¶
“A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods,” J. Andrew Grant, Barry T. Pickup and Anthony Nicholls, J. Comp. Chem, Vol 22, No.6, pgs 608-640, April 2001.
ZAP is, at its heart, a Poisson-Boltzmann (PB) solver. The Poisson equation describes how electrostatic fields change in a medium of varying dielectric, such as an organic molecule in water. The Boltzmann bit adds in the effect of mobile charge, e.g. salt. PB is an effective way to simulate the effects of water in biological systems. It relies on a charge description of a molecule, the designation of low (molecular) and high (solvent) dielectric regions and a description of an ion-accessible volume and produces a grid of electrostatic potentials. From this, transfer energies between different solvents, binding energies, pKa shifts, pI’s, solvent forces, electrostatic descriptors, solvent dipole moments, surface potentials and dielectric focussing can all be calculated. As electrostatics is one of the two principal components of molecular interaction (the other, of course, being shape), ZAP is OpenEye’s attempt to get it right.