Abstract
Abstract We present a numerical method for calculating the electrostatic potential of molecules in solution, using the linearized Poisson‐Boltzmann equation. The emphasis in this work is on applications to biological macromolecules. The accuracy of the method is assessed by comparisons with analytic solutions for the case of a single charge in a dielectric sphere (Tanford‐Kirkwood theory), which serves as a model for a macromolecule. We find that the solutions are generally accurate to within 5%. Larger errors occur close to the charge and the dielectric boundary, but the maximum error found at ion‐bonding distance (3 Å) from a charge close to the boundary (1 Å deep) is only ∼15%. Several algorithmic improvements, described here, contribute to the accuracy of the method. The programs involved compose a coherent software package, called Del Phi, which goes from a Brookhaven Protein Data Bank format file to calculated electrostatic fields.
Keywords
Poisson's equationElectrostaticsBoundary (topology)Charge (physics)DielectricWork (physics)Poisson–Boltzmann equationBoundary value problemStatistical physicsCharge densitySoftwareComputer sciencePhysicsComputational physicsAlgorithmIonQuantum mechanicsMathematicsMathematical analysis
Affiliated Institutions
Related Publications
Classical Electrostatics in Biology and Chemistry
A major revival in the use of classical electrostatics as an approach to the study of charged and polar molecules in aqueous solution has been made possible through the developm...
Electrostatics of nanosystems: Application to microtubules and the ribosome
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic ...
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
By using new methods for the parallel solution of elliptic partial differential equations, the teraflops computing power of massively parallel computers can be leveraged to perf...
An all-electron numerical method for solving the local density functional for polyatomic molecules
A method for accurate and efficient local density functional calculations (LDF) on molecules is described and presented with results. The method, Dmol for short, uses fast conve...
Medium effects on the molecular electronic structure. I. The formulation of a theory for the estimation of a molecular electronic structure surrounded by an anisotropic medium
A theory has been developed for estimation of the electronic structure of molecules embedded in an anisotropic (inhomogeneous) medium. It is assumed that the medium surrounding ...
Publication Info
- Year
- 1988
- Type
- article
- Volume
- 9
- Issue
- 4
- Pages
- 327-335
- Citations
- 1099
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
1099
OpenAlex
Cite This
Michael K. Gilson,
Kim A. Sharp,
Barry Honig
(1988).
Calculating the electrostatic potential of molecules in solution: Method and error assessment.
Journal of Computational Chemistry
, 9
(4)
, 327-335.
https://doi.org/10.1002/jcc.540090407
Identifiers
- DOI
- 10.1002/jcc.540090407