PARAMETER DEPENDENCE IN CONTINUUM ELECTROSTATIC CALCULATIONS : A STUDY USING PROTEIN SALT BRIDGES

Continuum electrostatic calculations were carried out for a data set of 21 salt bridges using three sets of parameters (charmm, parse, and a version of opls with slightly exaggerated atomic radii) and three representations of the dielectric boundary (approximate, exact, and smoothed versions of the analytic molecular surface). Comparisons of the overall results and a decomposition into terms due to desolvation, the direct salt bridge, and other interactions with the surrounding protein were used to analyze the effect of differences in parameter sets. It is concluded that (1) while numerical differences among the results can be significant, the underlying tension between desolvation penalty incurred and favorable interactions recovered upon folding is similar in all computations; (2) the largest variation occurs for the desolvation penalty, indicating the importance of fitting this property in parameter development; (3) the approximation of the molecular surface produces the largest desolvation penalties, ...