scholarly journals pKa Calculations with the Polarizable Drude Force Field and Poisson–Boltzmann Solvation Model

2020 ◽  
Vol 16 (7) ◽  
pp. 4655-4668 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Solvation Model ◽  
Pka Calculations ◽  
Poisson Boltzmann

scholarly journals Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model

2018 ◽  
Vol 39 (22) ◽  
pp. 1707-1719 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Fang-Yu Lin ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Implicit Solvation ◽  
Solvation Model ◽  
Implicit Solvation Model ◽  
Poisson Boltzmann

scholarly journals PypKa: a python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism

2018 ◽  
Author(s):  
Miguel Machuqueiro ◽  
Pedro Reis ◽  
Diogo Vila-Viçosa ◽  
Walter Rocchia
Keyword(s):  
Pka Calculations ◽  
Poisson Boltzmann

scholarly journals Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point-Charges

2021 ◽  
Author(s):  
Andreia Fortuna ◽  
Paulo J. Costa
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Field Methods ◽  
Amber Force Field ◽  
Center Point ◽  
Common Strategy ◽  
Poisson Boltzmann ◽  
General Force ◽  
Solvation Free Energies ◽  
Atomic Radii

<div>In force field methods, the usage of off-center point-charges, also called extra-points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently-bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics / molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X–EP distances. Poisson–Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (∆G solv ) of small molecules, often to compute binding free energies (∆G bind ) at the MM PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charges models and the lack of specific PB radii for halogens compatible with such implementations, in this work we assessed the performance of PBSA calculations for the estimation of ∆G solv values in water (∆G hyd ), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the General AMBER Force Field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM General Force Field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.</div>

scholarly journals Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point-Charges

2021 ◽  
Author(s):  
Andreia Fortuna ◽  
Paulo J. Costa
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Field Methods ◽  
Amber Force Field ◽  
Center Point ◽  
Common Strategy ◽  
Poisson Boltzmann ◽  
General Force ◽  
Solvation Free Energies ◽  
Atomic Radii

<div>In force field methods, the usage of off-center point-charges, also called extra-points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently-bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics / molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X–EP distances. Poisson–Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (∆G solv ) of small molecules, often to compute binding free energies (∆G bind ) at the MM PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charges models and the lack of specific PB radii for halogens compatible with such implementations, in this work we assessed the performance of PBSA calculations for the estimation of ∆G solv values in water (∆G hyd ), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the General AMBER Force Field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM General Force Field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.</div>

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