PsiRESP: calculating RESP charges with Psi4

Wang, Lily; O’Mara, Megan L.

doi:10.21105/joss.04100

Cited by 1 publication

(1 citation statement)

References 22 publications

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“…Optionally, the parametrization of new templates requires the QM engine ORCA, 92,93 autodE (used as an interface for QM engine), 94 and psiRESP, 81 and parametrization of the organic molecules requires AmberTools. 95 The code is built around four key objects (supramolecular_structure, new_template, metal_site, and patcher).…”

Section: Methodsmentioning

confidence: 99%

metallicious: Automated force-field parametrization of covalently bound metals for supramolecular structures

Piskorz,

Lee,

Zhan

et al. 2024

Preprint

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Metal ions play a central functional and structural role in many molecular structures, from small catalysts to metal-organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parametrization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parametrization of supramolecular structures. metallicious has been tested on diverse systems, including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters obtained from metallicious accurately reproduce the reference properties obtained from quantum calculations and crystal structures. MD simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with non-bonded and cationic dummy models. Overall, metallicious facilitates the setup of molecular dynamics (MD) of supramolecular systems simulations, providing insights into their dynamic properties and host-guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious)

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