MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations
Entity
UAM. Departamento de QuímicaPublisher
WileyDate
2022-12-12Citation
Journal of Computational Chemistry (2022): 1-18ISSN
0192-8651 (print); 1096-987X (online)Funded by
Spanish Ministry of Science and Innovation; MCIN/AEI, Grant/Award Numbers: PID2020-117806GA-I00, PID2019-110091GB-I00; María de Maeztu, Grant/Award Number: CEX2018-000805-M; Comunidad de Madrid, Grant/Award Number: 2018-T1/BMD-10261; Xunta de Galicia, Grant/Award Number: GRC2019/24; the European Social Fund; Spanish Ministry of Education and Vocational Training, Grant/Award Number: FPU19/02292; Universidade de Vigo, Grant/Award Number: PREUVIGO-21; Universidad Autonoma de MadridProject
Gobierno de España. PID2020-117806GA-I00Editor's Version
https://doi.org/10.1002/jcc.27018Subjects
Active Space; Electrostatic Embedding; Energy Decomposition Analysis; Molecular Dynamics; Open-source QM/MM software; Photochemistry; Reduction Potentials; QuímicaRights
© 2022 The Authors
Esta obra está bajo una licencia de Creative Commons Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional.
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
Files in this item
Google Scholar:Cárdenas, Gustavo
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Lucia Tamudo, Jesús
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Mateo de la Fuente, Henar
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Palmisano, Vito F.
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Anguita Ortiz, Nuria
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Ruano, Lorena
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Pérez Barcia, Alvaro
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Díaz-Tendero Victoria, Sergio
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Mandado, Marcos
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Nogueira Pérez, Juan José
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