Commun. Comput. Phys., 13 (2013), pp. 256-268.


DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

Lane W. Votapka 1, Luke Czapla 1, Maxim Zhenirovskyy 2, Rommie E. Amaro 1*

1 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
2 Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA.

Received 17 July 2011; Accepted (in revised version) 11 November 2011
Available online 12 June 2012
doi:10.4208/cicp.170711.111111s

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.


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PACS: 02.70.Ns
Key words: DelEnsembleElec, ensemble-averaged electrostatics, Poisson Boltzmann equation, DelPhi, molecular dynamics, influenza glycoproteins.

*Corresponding author.
Email: ramaro@ucsd.edu (R. E. Amaro)
 

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