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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ftpubmed:oai:pubmedcentral.nih.gov:10107847 2023-06-11T04:15:47+02:00 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. 2022-12-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10107847/ http://www.ncbi.nlm.nih.gov/pubmed/36507763 https://doi.org/10.1002/jcc.27018 en eng John Wiley & Sons, Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10107847/ http://www.ncbi.nlm.nih.gov/pubmed/36507763 http://dx.doi.org/10.1002/jcc.27018 © 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. J Comput Chem Research Articles Text 2022 ftpubmed https://doi.org/10.1002/jcc.27018 2023-04-23T00:50:27Z 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. Text Orca PubMed Central (PMC) Journal of Computational Chemistry 44 4 516 533 |
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Research Articles 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 |
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Research Articles |
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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. |
format |
Text |
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. |
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 |
John Wiley & Sons, Inc. |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10107847/ http://www.ncbi.nlm.nih.gov/pubmed/36507763 https://doi.org/10.1002/jcc.27018 |
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Orca |
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Orca |
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J Comput Chem |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10107847/ http://www.ncbi.nlm.nih.gov/pubmed/36507763 http://dx.doi.org/10.1002/jcc.27018 |
op_rights |
© 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. |
op_doi |
https://doi.org/10.1002/jcc.27018 |
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Journal of Computational Chemistry |
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44 |
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4 |
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516 |
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533 |
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1768372907653726208 |