Outline: we will use the SCS computer cluster to model the systems. CHARMM-GUI is developed by the Im Lab at the Lehigh University ( ). Note: NAMD and VMD are developed at the NIH Center for Macromolecular Modeling hosted at the University of Illinois at Urbana-Champaign ( ).
#Vmd measure rmsd Pc#
In a recent experimental study, the Fleming Lab (Johns Hopkins) used spontaneous folding of OmpLA into the membrane to design a hydrophobicity scale (Moon PC and Fleming KG, PNAS 108, 10174, 2011). The system of interest will be the outer membrane phospholipase A from E. This tutorial is designed to introduce the preparation, modeling, and analysis of membrane-protein system with molecular dynamics (MD) using NAMD, VMD, and CHARMM-GUI. School of Chemical Sciences, University of Illinois at Urbana-ChampaignĪugust 17, 2016, Edition 1.1. In a recent experimental study the Fleming Lab (Johns Hopkins) used spontaneous folding of OmpLA into the membrane to prepare a hydrophobicity scale (Moon PC and Fleming KG, PNAS 108, 10174, 2011)Įstimated time to complete this tutorial is 1.5 hr.īasics of membrane-protein interactions using molecular dynamics with NAMD, VMD, and CHARMM-GUI
coli (OmpLA, PDB ID 1QD5, Snijder HJ, …, Dijkstra BW, Nature, 401, 717, 1999). This tutorial is designed to introduce the preparation, modeling, and analysis of membrane-protein system with molecular dynamics (MD) using NAMD, VMD, and CHARMM-GUI.
0 kommentar(er)
