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PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent.
- 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.
- Subjects :
- Molecular Dynamics Simulation
Software
Solvents
Metals
Computational Chemistry
Subjects
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