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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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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. |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-10498442 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
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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