MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations
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 inpu...
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Online Access: | http://dx.doi.org/10.1002/jcc.27018 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.27018 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.27018 |
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crwiley:10.1002/jcc.27018 2024-09-15T18:28:57+00:00 MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations Cárdenas, Gustavo Lucia‐Tamudo, Jesús Mateo‐delaFuente, Henar Palmisano, Vito F. Anguita‐Ortiz, Nuria Ruano, Lorena Pérez‐Barcia, Álvaro Díaz‐Tendero, Sergio Mandado, Marcos Nogueira, Juan J. Ministerio de Ciencia e Innovación Comunidad de Madrid Xunta de Galicia European Social Fund Ministerio de Educación y Formación Profesional Universidade de Vigo Universidad Autónoma de Madrid 2022 http://dx.doi.org/10.1002/jcc.27018 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.27018 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.27018 en eng Wiley http://creativecommons.org/licenses/by-nc-nd/4.0/ Journal of Computational Chemistry volume 44, issue 4, page 516-533 ISSN 0192-8651 1096-987X journal-article 2022 crwiley https://doi.org/10.1002/jcc.27018 2024-08-06T04:12:09Z 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. Article in Journal/Newspaper Orca Wiley Online Library Journal of Computational Chemistry 44 4 516 533 |
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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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Ministerio de Ciencia e Innovación Comunidad de Madrid Xunta de Galicia European Social Fund Ministerio de Educación y Formación Profesional Universidade de Vigo Universidad Autónoma de Madrid |
format |
Article in Journal/Newspaper |
author |
Cárdenas, Gustavo Lucia‐Tamudo, Jesús Mateo‐delaFuente, Henar Palmisano, Vito F. Anguita‐Ortiz, Nuria Ruano, Lorena Pérez‐Barcia, Álvaro Díaz‐Tendero, Sergio Mandado, Marcos Nogueira, Juan J. |
spellingShingle |
Cárdenas, Gustavo Lucia‐Tamudo, Jesús Mateo‐delaFuente, Henar Palmisano, Vito F. Anguita‐Ortiz, Nuria Ruano, Lorena Pérez‐Barcia, Álvaro Díaz‐Tendero, Sergio Mandado, Marcos Nogueira, Juan J. MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations |
author_facet |
Cárdenas, Gustavo Lucia‐Tamudo, Jesús Mateo‐delaFuente, Henar Palmisano, Vito F. Anguita‐Ortiz, Nuria Ruano, Lorena Pérez‐Barcia, Álvaro Díaz‐Tendero, Sergio Mandado, Marcos Nogueira, Juan J. |
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://dx.doi.org/10.1002/jcc.27018 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.27018 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.27018 |
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Orca |
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Orca |
op_source |
Journal of Computational Chemistry volume 44, issue 4, page 516-533 ISSN 0192-8651 1096-987X |
op_rights |
http://creativecommons.org/licenses/by-nc-nd/4.0/ |
op_doi |
https://doi.org/10.1002/jcc.27018 |
container_title |
Journal of Computational Chemistry |
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44 |
container_issue |
4 |
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516 |
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533 |
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1810470378316759040 |