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Efficient minimization of multipole electrostatic potentials in torsion space
The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895050/ https://www.ncbi.nlm.nih.gov/pubmed/29641557 http://dx.doi.org/10.1371/journal.pone.0195578 |
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author | Bodmer, Nicholas K. Havranek, James J. |
author_facet | Bodmer, Nicholas K. Havranek, James J. |
author_sort | Bodmer, Nicholas K. |
collection | PubMed |
description | The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom. |
format | Online Article Text |
id | pubmed-5895050 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-58950502018-05-04 Efficient minimization of multipole electrostatic potentials in torsion space Bodmer, Nicholas K. Havranek, James J. PLoS One Research Article The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom. Public Library of Science 2018-04-11 /pmc/articles/PMC5895050/ /pubmed/29641557 http://dx.doi.org/10.1371/journal.pone.0195578 Text en © 2018 Bodmer, Havranek http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Bodmer, Nicholas K. Havranek, James J. Efficient minimization of multipole electrostatic potentials in torsion space |
title | Efficient minimization of multipole electrostatic potentials in torsion space |
title_full | Efficient minimization of multipole electrostatic potentials in torsion space |
title_fullStr | Efficient minimization of multipole electrostatic potentials in torsion space |
title_full_unstemmed | Efficient minimization of multipole electrostatic potentials in torsion space |
title_short | Efficient minimization of multipole electrostatic potentials in torsion space |
title_sort | efficient minimization of multipole electrostatic potentials in torsion space |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895050/ https://www.ncbi.nlm.nih.gov/pubmed/29641557 http://dx.doi.org/10.1371/journal.pone.0195578 |
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