Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Bodmer, Nicholas K., Havranek, James J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
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
_version_ 1783313592244764672
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
work_keys_str_mv AT bodmernicholask efficientminimizationofmultipoleelectrostaticpotentialsintorsionspace
AT havranekjamesj efficientminimizationofmultipoleelectrostaticpotentialsintorsionspace