ArticleJournal of computational chemistry2023
MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.
Article in Journal of computational chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Computational design of an improved photoswitchable psychedelic based on light absorption, membrane permeation and protein binding.Physical chemistry chemical physics : PCCP · 2025Article
- SparcleQC: Automated Input File Creation for QM/MM Studies of Protein:Ligand Complexes.Journal of chemical information and modeling · 2025Article
- Attosecond impulsive stimulated X-ray Raman scattering in liquid water.Science advances · 2024Article
- Charge Transfer Mechanism in Guanine-Based Self-Assembled Monolayers on a Gold Surface.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches.Journal of chemical information and modeling · 2024Article
- Effect of stacking interactions on charge transfer states in photoswitches interacting with ion channels.Physical chemistry chemical physics : PCCP · 2023Article
- Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis.Journal of chemical information and modeling · 2023Article
- MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.Journal of computational chemistry · 2023Article
- On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis.Membranes · 2022Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.