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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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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. |
format | Online Article Text |
id | pubmed-9921782 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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