Journal
COMMUNICATIONS IN COMPUTATIONAL PHYSICS
Volume 13, Issue 1, Pages 256-268Publisher
GLOBAL SCIENCE PRESS
DOI: 10.4208/cicp.170711.111111s
Keywords
DelEnsembleElec; ensemble-averaged electrostatics; Poisson Boltzmann equation; DelPhi; molecular dynamics; influenza glycoproteins
Categories
Funding
- National Institutes of Health [1-DP2-OD007237]
- NSF [LRAC CHE060073N]
- Institute of General Medical Sciences, National Institutes of Health [1R01GM093937-01]
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available