MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations
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 f...
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ftuamadrid:oai:repositorio.uam.es:10486/705772 2023-05-15T17:53:59+02:00 MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations Cárdenas, Gustavo Lucia Tamudo, Jesús Mateo de la Fuente, Henar Palmisano, Vito F. Anguita Ortiz, Nuria Ruano, Lorena Pérez Barcia, Alvaro Díaz-Tendero Victoria, Sergio Mandado, Marcos Nogueira Pérez, Juan José UAM. Departamento de Química 2022-12-22T07:42:02Z application/pdf http://hdl.handle.net/10486/705772 eng eng Wiley Journal of Computational Chemistry https://doi.org/10.1002/jcc.27018 Gobierno de España. PID2020-117806GA-I00 Journal of Computational Chemistry (2022): 1-18 0192-8651 (print) 1096-987X (online) http://hdl.handle.net/10486/705772 1 18 © 2022 The Authors Reconocimiento – NoComercial – SinObraDerivada openAccess Active Space Electrostatic Embedding Energy Decomposition Analysis Molecular Dynamics Open-source QM/MM software Photochemistry Reduction Potentials Química article info:eu-repo/semantics/publishedVersion 2022 ftuamadrid https://doi.org/10.1002/jcc.27018 2022-12-28T00:12:31Z 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 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 Madrid Article in Journal/Newspaper Orca Universidad Autónoma de Madrid (UAM): Biblos-e Archivo Journal of Computational Chemistry 44 4 516 533 |
institution |
Open Polar |
collection |
Universidad Autónoma de Madrid (UAM): Biblos-e Archivo |
op_collection_id |
ftuamadrid |
language |
English |
topic |
Active Space Electrostatic Embedding Energy Decomposition Analysis Molecular Dynamics Open-source QM/MM software Photochemistry Reduction Potentials Química |
spellingShingle |
Active Space Electrostatic Embedding Energy Decomposition Analysis Molecular Dynamics Open-source QM/MM software Photochemistry Reduction Potentials Química Cárdenas, Gustavo Lucia Tamudo, Jesús Mateo de la Fuente, Henar Palmisano, Vito F. Anguita Ortiz, Nuria Ruano, Lorena Pérez Barcia, Alvaro Díaz-Tendero Victoria, Sergio Mandado, Marcos Nogueira Pérez, Juan José MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
topic_facet |
Active Space Electrostatic Embedding Energy Decomposition Analysis Molecular Dynamics Open-source QM/MM software Photochemistry Reduction Potentials Química |
description |
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 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 Madrid |
author2 |
UAM. Departamento de Química |
format |
Article in Journal/Newspaper |
author |
Cárdenas, Gustavo Lucia Tamudo, Jesús Mateo de la Fuente, Henar Palmisano, Vito F. Anguita Ortiz, Nuria Ruano, Lorena Pérez Barcia, Alvaro Díaz-Tendero Victoria, Sergio Mandado, Marcos Nogueira Pérez, Juan José |
author_facet |
Cárdenas, Gustavo Lucia Tamudo, Jesús Mateo de la Fuente, Henar Palmisano, Vito F. Anguita Ortiz, Nuria Ruano, Lorena Pérez Barcia, Alvaro Díaz-Tendero Victoria, Sergio Mandado, Marcos Nogueira Pérez, Juan José |
author_sort |
Cárdenas, Gustavo |
title |
MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
title_short |
MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
title_full |
MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
title_fullStr |
MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
title_full_unstemmed |
MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
title_sort |
mobiotools: a toolkit to setup quantum mechanics/molecular mechanics calculations |
publisher |
Wiley |
publishDate |
2022 |
url |
http://hdl.handle.net/10486/705772 |
genre |
Orca |
genre_facet |
Orca |
op_relation |
Journal of Computational Chemistry https://doi.org/10.1002/jcc.27018 Gobierno de España. PID2020-117806GA-I00 Journal of Computational Chemistry (2022): 1-18 0192-8651 (print) 1096-987X (online) http://hdl.handle.net/10486/705772 1 18 |
op_rights |
© 2022 The Authors Reconocimiento – NoComercial – SinObraDerivada openAccess |
op_doi |
https://doi.org/10.1002/jcc.27018 |
container_title |
Journal of Computational Chemistry |
container_volume |
44 |
container_issue |
4 |
container_start_page |
516 |
op_container_end_page |
533 |
_version_ |
1766161704215904256 |