Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.

ABSTRACT: We investigate the influence of three common definitions of the solute/solvent dielectric boundary (DB) on the accuracy of the electrostatic solvation energy ΔGel computed within the Poisson Boltzmann and the generalized Born models of implicit solvation. The test structures include small molecules, peptides and small proteins; explicit solvent ΔGel are used as accuracy reference. For common atomic radii sets BONDI, PARSE (and ZAP9 for small molecules) the use of van der Waals (vdW) DB results, on average, in considerably larger errors in ΔGel than the molecular surface (MS) DB. The optimal probe radius ρw for which the MS DB yields the most accurate ΔGel varies considerably between structure types. The solvent accessible surface (SAS) DB becomes optimal at ρw ~ 0.2 Å (exact value is sensi

SUBMITTER: Onufriev AV 

PROVIDER: S-EPMC4520245 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature