CONDUCTOR, a fast, efficient and robust tool for continuum solvation computations for macromolecules

This introduces CONDUCTOR, an algorithm for computing solvation effects for large molecules using the continuum approximation. While we represent electrostatic polarization by the mechanism of induced surface charge, we avoid the explicit computation of a Green function as found with the Boundary Element Method (BEM). Instead, we assume as a starting point the conducting approximation for aqueous solvent, and adjust the induced polarization charge defined on the molecular surface, so as to force the electric potential to zero at field points positioned on the solvent side of the surface. The charge density for finite external dielectric constant can then be approximated using a simple perturbation approach. The reaction field arising from the induced charge distribution is used to compute the contribution of solvent to the electrostatic potential and forces for the molecular fixed charges. The method is robust, being relatively insensitive to small defects or singularities in the molecular surface, and can be extended to periodic structures such as membranes. Computations for proteins with nearly 300 residues can be carried out in about ten minutes on inexpensive server hardware. We compare the results of our new approach to the conventional Boundary Element Method, and find them equivalent, and by some measures superior, to the BEM, and achieved with much less computational expense.