PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent
[Image: see text] We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used com...
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ftpubmed:oai:pubmedcentral.nih.gov:10498442 2023-10-09T21:55:03+02:00 PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent Talmazan, R. A. Podewitz, M. 2023-08-22 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498442/ http://www.ncbi.nlm.nih.gov/pubmed/37606893 https://doi.org/10.1021/acs.jcim.3c00798 en eng American Chemical Society http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498442/ http://www.ncbi.nlm.nih.gov/pubmed/37606893 http://dx.doi.org/10.1021/acs.jcim.3c00798 © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). J Chem Inf Model Text 2023 ftpubmed https://doi.org/10.1021/acs.jcim.3c00798 2023-09-17T00:59:02Z [Image: see text] We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge. Text Orca PubMed Central (PMC) Journal of Chemical Information and Modeling 63 17 5400 5407 |
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[Image: see text] We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge. |
format |
Text |
author |
Talmazan, R. A. Podewitz, M. |
spellingShingle |
Talmazan, R. A. Podewitz, M. PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent |
author_facet |
Talmazan, R. A. Podewitz, M. |
author_sort |
Talmazan, R. A. |
title |
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent |
title_short |
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent |
title_full |
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent |
title_fullStr |
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent |
title_full_unstemmed |
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent |
title_sort |
pyconsolv: a python package for conformer generation of (metal-containing) systems in explicit solvent |
publisher |
American Chemical Society |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498442/ http://www.ncbi.nlm.nih.gov/pubmed/37606893 https://doi.org/10.1021/acs.jcim.3c00798 |
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Orca |
genre_facet |
Orca |
op_source |
J Chem Inf Model |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498442/ http://www.ncbi.nlm.nih.gov/pubmed/37606893 http://dx.doi.org/10.1021/acs.jcim.3c00798 |
op_rights |
© 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
op_doi |
https://doi.org/10.1021/acs.jcim.3c00798 |
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Journal of Chemical Information and Modeling |
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63 |
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17 |
container_start_page |
5400 |
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5407 |
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1779318827065016320 |