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DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

Published online by Cambridge University Press:  03 June 2015

Lane W. Votapka ,
Luke Czapla ,
Maxim Zhenirovskyy  and
Rommie E. Amaro
Lane W. Votapka
Affiliation:
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
Luke Czapla
Affiliation:
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
Maxim Zhenirovskyy
Affiliation:
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
Rommie E. Amaro*
Affiliation:
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
*
*Corresponding author.Email:ramaro@ucsd.edu
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Abstract

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented. The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented. This new tool is applied to systems of current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

Keywords

02.70.NsDelEnsembleElecensemble-averaged electrostaticsPoisson Boltzmann equationDelPhimolecular dynamicsinfluenza glycoproteins
Type
Research Article
Information
Communications in Computational Physics , Volume 13 , Issue 1 , January 2013 , pp. 256 - 268
Copyright
Copyright © Global Science Press Limited 2013

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