Monovalent and Divalent Salt Effects on Electrostatic Free Energies Defined by the Nonlinear Poisson−Boltzmann Equation:  Application to DNA Binding Reactions

1997 ◽  
Vol 101 (44) ◽  
pp. 9113-9118 ◽  
Author(s):  
Shu-wen W. Chen ◽  
Barry Honig
Keyword(s):  
Boltzmann Equation ◽  
Dna Binding ◽  
Free Energies ◽  
Salt Effects ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Accurate estimation of electrostatic binding energy with Poisson-Boltzmann equation solver DelPhi program

2016 ◽  
Vol 15 (08) ◽  
pp. 1650071
Author(s):  
Anbang Li ◽  
Kaifu Gao
Keyword(s):  
Boltzmann Equation ◽  
Binding Energy ◽  
Binding Free Energy ◽  
Molecular Surface ◽  
Accurate Estimation ◽  
Free Energies ◽  
Grid Spacing ◽  
Electrostatic Binding ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Poisson–Boltzmann (PB) model is a widely used implicit solvent approximation in biophysical modeling because of its ability to provide accurate and reliable PB electrostatic salvation free energies ([Formula: see text] as well as electrostatic binding free energy ([Formula: see text] estimations. However, a recent study has warned that the 0.5[Formula: see text]Å grid spacing which is normally adopted can produce unacceptable errors in [Formula: see text] estimation with the solvent excluded surface (SES) (Harris RC, Boschitsch AH and Fenley MO, Influence of grid spacing in Poisson–Boltzmann equation binding energy estimation, J Chem Theory Comput 19: 3677–3685, 2013). In this work, we investigate the grid dependence of the widely used PB solver DelPhi v6.2 with molecular surface (MS) for estimating both electrostatic solvation free energies and electrostatic binding free energies. Our results indicate that, for the molecular complex and components the absolute errors of [Formula: see text] are smaller than that of [Formula: see text], and grid spacing of 0.8[Formula: see text]Å with DelPhi program ensures the accuracy and reliability of [Formula: see text]; however, the accuracy of [Formula: see text] largely relies on the order of magnitude of [Formula: see text] itself rather than that of [Formula: see text] or [Formula: see text]. Our findings suggest that grid spacing of 0.5[Formula: see text]Å is enough to produce accurate [Formula: see text] for molecules whose [Formula: see text] are large, but finer grids are needed when [Formula: see text] is very small.

scholarly journals Monte Carlo methods for linear and non-linear Poisson-Boltzmann equation

2015 ◽  
Vol 48 ◽  
pp. 420-446 ◽  
Author(s):  
Mireille Bossy ◽  
Nicolas Champagnat ◽  
Hélène Leman ◽  
Sylvain Maire ◽  
Laurent Violeau ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Boltzmann Equation ◽  
Monte Carlo Methods ◽  
Non Linear ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation
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