Submitted by pogorelo on Mon, 08/17/2015 - 23:54
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. The system of interest will be the outer membrane phospholipase A from E. coli (OmpLA, PDB ID 1QD5, Snijder HJ, …, Dijkstra BW, Nature, 401, 717, 1999). 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)
Estimated time to complete this tutorial is 1.5 hr.