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 ...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.展开更多
Here we report a web server,the DelPhi web server,which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions,and dielectric map.The server p...Here we report a web server,the DelPhi web server,which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions,and dielectric map.The server provides extra services to fix structural defects,as missing atoms in the structural file and allows for generation of missing hydrogen atoms.The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22,Amber98 or OPLS.Upon completion of the calculations,the user is given option to download fixed and protonated structural file,together with the parameter and Delphi output files for further analysis.Utilizing Jmol viewer,the user can see the corresponding structural file,to manipulate it and to change the presentation.In addition,if the potential map is requested to be calculated,the potential can be mapped onto the molecule surface.The DelPhi web server is available from http://compbio.clemson.edu/delphi webserver.展开更多
基金funded in part by the National Institutes of Health through the NIH Director’s New Innovator Award Program 1-DP2-OD007237through 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.
文摘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supported by a grant from the Institute of General Medical Sciences,National Institutes of Health,award number 1R01GM093937.
文摘Here we report a web server,the DelPhi web server,which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions,and dielectric map.The server provides extra services to fix structural defects,as missing atoms in the structural file and allows for generation of missing hydrogen atoms.The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22,Amber98 or OPLS.Upon completion of the calculations,the user is given option to download fixed and protonated structural file,together with the parameter and Delphi output files for further analysis.Utilizing Jmol viewer,the user can see the corresponding structural file,to manipulate it and to change the presentation.In addition,if the potential map is requested to be calculated,the potential can be mapped onto the molecule surface.The DelPhi web server is available from http://compbio.clemson.edu/delphi webserver.
