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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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Detalles Bibliográficos
Autores principales: Talmazan, R. A., Podewitz, M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498442/
https://www.ncbi.nlm.nih.gov/pubmed/37606893
http://dx.doi.org/10.1021/acs.jcim.3c00798
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author Talmazan, R. A.
Podewitz, M.
author_facet Talmazan, R. A.
Podewitz, M.
author_sort Talmazan, R. A.
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description [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.
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spelling pubmed-104984422023-09-14 PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent Talmazan, R. A. Podewitz, M. J Chem Inf Model [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. American Chemical Society 2023-08-22 /pmc/articles/PMC10498442/ /pubmed/37606893 http://dx.doi.org/10.1021/acs.jcim.3c00798 Text en © 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/).
spellingShingle Talmazan, R. A.
Podewitz, M.
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent
title 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_short 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
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498442/
https://www.ncbi.nlm.nih.gov/pubmed/37606893
http://dx.doi.org/10.1021/acs.jcim.3c00798
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