GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations
Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the s...
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| Vydáno v: | Journal of computational chemistry Ročník 34; číslo 25; s. 2190 - 2196 |
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| Médium: | Journal Article |
| Jazyk: | angličtina |
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United States
Blackwell Publishing Ltd
30.09.2013
Wiley Subscription Services, Inc Wiley |
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| ISSN: | 0192-8651, 1096-987X, 1096-987X |
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| Abstract | Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open‐source graphical plug‐in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. © 2013 Wiley Periodicals, Inc.
This article describes the implementation and the main capabilities of GTKDynamo, a general‐purpose, open‐source graphical interface that combines the molecular modeling program, pDynamo, with the molecular visualizer, PyMOL. The design of the interface places particular emphasis on facilitating the determination of reaction pathways in biological systems using hybrid quantum chemical/molecular mechanical (QC/MM) potentials. |
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| AbstractList | Hybrid quantum chemical (QC)/molecular mechanical (MM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions, that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use we have developed an open-source graphical plug-in, GTKDynamo, that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. [PUBLICATION ABSTRACT] Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations.Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open‐source graphical plug‐in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. © 2013 Wiley Periodicals, Inc. This article describes the implementation and the main capabilities of GTKDynamo, a general‐purpose, open‐source graphical interface that combines the molecular modeling program, pDynamo, with the molecular visualizer, PyMOL. The design of the interface places particular emphasis on facilitating the determination of reaction pathways in biological systems using hybrid quantum chemical/molecular mechanical (QC/MM) potentials. |
| Author | Assirati, Lucas Bachega, Leonardo R. Bachega, José Fernando R. Timmers, Luís Fernando S. M. Wymore, Troy Field, Martin J. |
| AuthorAffiliation | b Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO) - Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM) - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre - RS, Brazil a Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil d DYNAMO/DYNAMOP, Institut de Biologie Structurale – Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France (UMR 5075 – CEA/CNRS/UJF Grenoble I) e Pittsburgh Supercomputing Center, Pittsburgh, USA c School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907 USA |
| AuthorAffiliation_xml | – name: a Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil – name: e Pittsburgh Supercomputing Center, Pittsburgh, USA – name: b Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO) - Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM) - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre - RS, Brazil – name: c School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907 USA – name: d DYNAMO/DYNAMOP, Institut de Biologie Structurale – Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France (UMR 5075 – CEA/CNRS/UJF Grenoble I) |
| Author_xml | – sequence: 1 givenname: José Fernando R. surname: Bachega fullname: Bachega, José Fernando R. email: ferbachega@gmail.com organization: Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, CEP 13566-590, São Carlos-SP, Brazil – sequence: 2 givenname: Luís Fernando S. M. surname: Timmers fullname: Timmers, Luís Fernando S. M. organization: Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO)-Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM) - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre-RS, Brazil – sequence: 3 givenname: Lucas surname: Assirati fullname: Assirati, Lucas organization: Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, CEP 13566-590, São Carlos-SP, Brazil – sequence: 4 givenname: Leonardo R. surname: Bachega fullname: Bachega, Leonardo R. organization: School of Electrical and Computer Engineering, Purdue University, Indiana, 47907, West Lafayette – sequence: 5 givenname: Martin J. surname: Field fullname: Field, Martin J. organization: DYNAMO/DYNAMOP, Institut de Biologie Structurale-Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France (UMR 5075-CEA/CNRS/UJF Grenoble I) – sequence: 6 givenname: Troy surname: Wymore fullname: Wymore, Troy organization: Pittsburgh Supercomputing Center, National Resource for Biomedical Supercomputing Department, Pittsburgh |
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| Snippet | Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying... Hybrid quantum chemical (QC)/molecular mechanical (MM) potentials are very powerful tools for molecular simulation. They are especially useful for studying... |
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| SubjectTerms | Biochemistry, Molecular Biology Chemicals graphical plug-in hybrid quantum chemical/molecular mechanical potentials Life Sciences Molecular Dynamics Simulation molecular simulation Molecular structure pDynamo molecular modeling package PyMOL molecular visualization package Python scripting language Quantum Theory Simulation Software Software - standards Structural Biology |
| Title | GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations |
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| Volume | 34 |
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