Calculating the electrostatic potential of molecules in solution: Method and error assessment

✍ Scribed by Michael K. Gilson; Kim A. Sharp; Barry H. Honig

• Publisher: John Wiley and Sons
• Year: 1988
• Tongue: English
• Weight: 795 KB
• Volume: 9
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540090407

✦ Synopsis

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 A) from a charge close to the boundary (1 A 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.