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Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches
Optimized link bond parameters for the C(α)—C(β) bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self‐consistent charge density functional tight‐binding), SCC DFTB/3ob and GFNn‐xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B fo...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9314059/ https://www.ncbi.nlm.nih.gov/pubmed/35239208 http://dx.doi.org/10.1002/jcc.26830 |
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author | Gallmetzer, Hans Georg Hofer, Thomas S. |
author_facet | Gallmetzer, Hans Georg Hofer, Thomas S. |
author_sort | Gallmetzer, Hans Georg |
collection | PubMed |
description | Optimized link bond parameters for the C(α)—C(β) bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self‐consistent charge density functional tight‐binding), SCC DFTB/3ob and GFNn‐xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B force fields. The resulting parameter sets have been compared to newly calculated reference data obtained via resolution‐of‐identity 2nd order Møller–Plesset perturbation theory. The data collected in this work suggests that the optimized values in this study provide a more suitable setup of the QM/MM link bonds compared to the use of a single global setting applied to every amino acid fragmented by the QM/MM interface. The results also imply that a transfer of the ideal link bond settings between different levels of theory is not advised. In contrast, virtually identical parameters were obtained in calculations employing different variants of the AMBER force field. Considering the increasing success of tight binding based approaches being inter alia a results of their exceptional accuracy/effort ratio the provided collection of link atoms parameters provides a valuable resource for QM/MM studies of biomacromolecular systems as demonstrated in an exemplary QM/MM MD simulation of the β‐amyloid/Zn(2+) complex. |
format | Online Article Text |
id | pubmed-9314059 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-93140592022-07-30 Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches Gallmetzer, Hans Georg Hofer, Thomas S. J Comput Chem Research Articles Optimized link bond parameters for the C(α)—C(β) bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self‐consistent charge density functional tight‐binding), SCC DFTB/3ob and GFNn‐xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B force fields. The resulting parameter sets have been compared to newly calculated reference data obtained via resolution‐of‐identity 2nd order Møller–Plesset perturbation theory. The data collected in this work suggests that the optimized values in this study provide a more suitable setup of the QM/MM link bonds compared to the use of a single global setting applied to every amino acid fragmented by the QM/MM interface. The results also imply that a transfer of the ideal link bond settings between different levels of theory is not advised. In contrast, virtually identical parameters were obtained in calculations employing different variants of the AMBER force field. Considering the increasing success of tight binding based approaches being inter alia a results of their exceptional accuracy/effort ratio the provided collection of link atoms parameters provides a valuable resource for QM/MM studies of biomacromolecular systems as demonstrated in an exemplary QM/MM MD simulation of the β‐amyloid/Zn(2+) complex. John Wiley & Sons, Inc. 2022-03-03 2022-04-30 /pmc/articles/PMC9314059/ /pubmed/35239208 http://dx.doi.org/10.1002/jcc.26830 Text en © 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Gallmetzer, Hans Georg Hofer, Thomas S. Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches |
title | Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches |
title_full | Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches |
title_fullStr | Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches |
title_full_unstemmed | Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches |
title_short | Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches |
title_sort | probing the range of applicability of structure‐ and energy‐adjusted qm/mm link bonds ii: optimized link bond parameters for density functional tight binding approaches |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9314059/ https://www.ncbi.nlm.nih.gov/pubmed/35239208 http://dx.doi.org/10.1002/jcc.26830 |
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