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...
| Published in: | Journal of Chemical Information and Modeling |
|---|---|
| Main Authors: | , |
| Format: | Text |
| Language: | English |
| Published: |
American Chemical Society
2023
|
| Subjects: | |
| Online Access: | 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 |
| Summary: | [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. |
|---|