Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

2012 ◽  
Vol 8 (8) ◽  
pp. 2553-2558 ◽  
Author(s):  
Devleena Shivakumar ◽  
Edward Harder ◽  
Wolfgang Damm ◽  
Richard A. Friesner ◽  
Woody Sherman
Keyword(s):  
Force Field ◽  
Next Generation ◽  
Free Energies ◽  
Solvation Free Energies

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field

2014 ◽  
Vol 10 (8) ◽  
pp. 3570-3577 ◽  
Author(s):  
Silvia A. Martins ◽  
Sergio F. Sousa ◽  
Maria João Ramos ◽  
Pedro A. Fernandes
Keyword(s):  
Force Field ◽  
Thermodynamic Integration ◽  
Free Energies ◽  
Amber Force Field ◽  
Solvation Free Energies

scholarly journals Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

2016 ◽  
Vol 37 (32) ◽  
pp. 2749-2758 ◽  
Author(s):  
Noor Asidah Mohamed ◽  
Richard T. Bradshaw ◽  
Jonathan W. Essex
Keyword(s):  
Force Field ◽  
Small Molecules ◽  
Free Energies ◽  
Polarizable Force Field ◽  
Solvation Free Energies

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

2010 ◽  
Vol 6 (5) ◽  
pp. 1509-1519 ◽  
Author(s):  
Devleena Shivakumar ◽  
Joshua Williams ◽  
Yujie Wu ◽  
Wolfgang Damm ◽  
John Shelley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Force Field ◽  
Free Energy Perturbation ◽  
Free Energies ◽  
Energy Perturbation ◽  
Solvation Free Energies

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>

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>

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

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