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PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent.

Authors :
Talmazan RA
Podewitz M
Source :
Journal of chemical information and modeling [J Chem Inf Model] 2023 Sep 11; Vol. 63 (17), pp. 5400-5407. Date of Electronic Publication: 2023 Aug 22.
Publication Year :
2023

Abstract

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.

Details

Language :
English
ISSN :
1549-960X
Volume :
63
Issue :
17
Database :
MEDLINE
Journal :
Journal of chemical information and modeling
Publication Type :
Academic Journal
Accession number :
37606893
Full Text :
https://doi.org/10.1021/acs.jcim.3c00798