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Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction

Hydration free energies of small molecules are commonly used as benchmarks for solvation models. However, errors in predicting hydration free energies are partially due to the force fields used and not just the solvation model. To address this, we have used the 3D reference interaction site model (3...

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Autores principales: Casillas, Lizet, Grigorian, Vahe M., Luchko, Tyler
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9921782/
https://www.ncbi.nlm.nih.gov/pubmed/36770599
http://dx.doi.org/10.3390/molecules28030925
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author Casillas, Lizet
Grigorian, Vahe M.
Luchko, Tyler
author_facet Casillas, Lizet
Grigorian, Vahe M.
Luchko, Tyler
author_sort Casillas, Lizet
collection PubMed
description Hydration free energies of small molecules are commonly used as benchmarks for solvation models. However, errors in predicting hydration free energies are partially due to the force fields used and not just the solvation model. To address this, we have used the 3D reference interaction site model (3D-RISM) of molecular solvation and existing benchmark explicit solvent calculations with a simple element count correction (ECC) to identify problems with the non-bond parameters in the general AMBER force field (GAFF). 3D-RISM was used to calculate hydration free energies of all 642 molecules in the FreeSolv database, and a partial molar volume correction (PMVC), ECC, and their combination (PMVECC) were applied to the results. The PMVECC produced a mean unsigned error of [Formula: see text] and root mean squared error of [Formula: see text] , better than the benchmark explicit solvent calculations from FreeSolv, and required less than 15 s of computing time per molecule on a single CPU core. Importantly, parameters for PMVECC showed systematic errors for molecules containing Cl, Br, I, and P. Applying ECC to the explicit solvent hydration free energies found the same systematic errors. The results strongly suggest that some small adjustments to the Lennard–Jones parameters for GAFF will lead to improved hydration free energy calculations for all solvent models.
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spelling pubmed-99217822023-02-12 Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction Casillas, Lizet Grigorian, Vahe M. Luchko, Tyler Molecules Article Hydration free energies of small molecules are commonly used as benchmarks for solvation models. However, errors in predicting hydration free energies are partially due to the force fields used and not just the solvation model. To address this, we have used the 3D reference interaction site model (3D-RISM) of molecular solvation and existing benchmark explicit solvent calculations with a simple element count correction (ECC) to identify problems with the non-bond parameters in the general AMBER force field (GAFF). 3D-RISM was used to calculate hydration free energies of all 642 molecules in the FreeSolv database, and a partial molar volume correction (PMVC), ECC, and their combination (PMVECC) were applied to the results. The PMVECC produced a mean unsigned error of [Formula: see text] and root mean squared error of [Formula: see text] , better than the benchmark explicit solvent calculations from FreeSolv, and required less than 15 s of computing time per molecule on a single CPU core. Importantly, parameters for PMVECC showed systematic errors for molecules containing Cl, Br, I, and P. Applying ECC to the explicit solvent hydration free energies found the same systematic errors. The results strongly suggest that some small adjustments to the Lennard–Jones parameters for GAFF will lead to improved hydration free energy calculations for all solvent models. MDPI 2023-01-17 /pmc/articles/PMC9921782/ /pubmed/36770599 http://dx.doi.org/10.3390/molecules28030925 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Casillas, Lizet
Grigorian, Vahe M.
Luchko, Tyler
Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction
title Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction
title_full Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction
title_fullStr Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction
title_full_unstemmed Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction
title_short Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction
title_sort identifying systematic force field errors using a 3d-rism element counting correction
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9921782/
https://www.ncbi.nlm.nih.gov/pubmed/36770599
http://dx.doi.org/10.3390/molecules28030925
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