scholarly journals Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field

2016 ◽  
Vol 12 (8) ◽  
pp. 3871-3883 ◽  
Author(s):  
Richard T. Bradshaw ◽  
Jonathan W. Essex
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Free Energy Calculations ◽  
Hydration Free Energy ◽  
Polarizable Force Field ◽  
Energy Calculations

scholarly journals Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

2021 ◽  
Author(s):  
Lauren Nelson ◽  
Sofia Bariami ◽  
Chris Ringrose ◽  
Joshua Horton ◽  
Vadiraj Kurdekar ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
High Throughput ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Simulation Package ◽  
Alchemical Free Energy Calculations

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field approach has been developed to facilitate the automated derivation of potential energy function parameters for modelling protein-ligand binding. To date the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free energy calculation molecular dynamics simulation package SOMD. The implementation is validated by demonstrating the reproducibility of absolute hydration free energies computed with the QUBE force field across the SOMD and GROMACS software packages. We further demonstrate, by way of a case study involving two series of non-nucleoside inhibitors of HIV-1 reverse transcriptase, that the availability of QUBE in a modern simulation package that makes efficient use of GPU acceleration will facilitate high-throughput alchemical free energy calculations.</p></div></div></div>

scholarly journals Multipole electrostatics in hydration free energy calculations

2010 ◽  
Vol 32 (5) ◽  
pp. 967-977 ◽  
Author(s):  
Yue Shi ◽  
Chuanjie Wu ◽  
Jay W. Ponder ◽  
Pengyu Ren
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Hydration Free Energy ◽  
Energy Calculations

A hybrid quantum mechanical molecular mechanical method: Application to hydration free energy calculations

2002 ◽  
Vol 117 (6) ◽  
pp. 2762-2770 ◽  
Author(s):  
Tamer Shoeib ◽  
Giuseppe D. Ruggiero ◽  
K. W. Michael Siu ◽  
Alan C. Hopkinson ◽  
Ian H. Williams
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Quantum Mechanical ◽  
Hydration Free Energy ◽  
Mechanical Method ◽  
Energy Calculations

Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

2005 ◽  
Vol 103 (14) ◽  
pp. 1961-1969 ◽  
Author(s):  
Yu Zhou ◽  
Chris Oostenbrink ◽  
Wilfred F. Van Gunsteren ◽  
Wilfred R. Hagen ◽  
Simon W. De Leeuw ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Relative Stability ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Force Field Parameters

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An OTFP Approach

2019 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Free Energy Calculations ◽  
Partial Charge ◽  
Experimental Uncertainty ◽  
Hydration Free Energy ◽  
Energy Calculations ◽  
Lennard Jones ◽  
Partial Charges ◽  
The Cost

We present a methodology using fixed charge force–fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges use QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug–like molecules.We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential(RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an AAD that is 2.98 kJ·mol−1(0.71 kcal·mol−1) lower than AM1–BCC. AM1–BCC is within experimental uncertainty on 10% of thedata compared to 40% with our method. We conjecture that results can be further improved by using Lennard–Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.<br>

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