摘要
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.
基金
funded in part by the National Institutes of Health through the NIH Director’s New Innovator Award Program 1-DP2-OD007237
through the NSF TeraGrid Supercomputer resources grant LRAC CHE060073N to R.E.A.
supported by a grant from the Institute of General Medical Sciences,National Institutes of Health,award number 1R01GM093937-01.
