#VMD TUTORIAL FILES GENERATOR#

Open the CHARMM-GUI website () and go to Input Generator –> Membrane Builder –> Bilayer Builder.ġ.1 CHARMM-GUI: load, analyze, and position PDBĬHARMM-GUI provides choice for protein orientation in the membrane. Small modifications might be needed when used on other computers. This tutorial can be completed on iMacs in the SCS VizLab (151 Noyes Lab) or with personal computers with Windows or Mac OS. MobaXTerm for a Windows machine), and CHARMM-GUI web server. Personal computer: Terminal (Mac OSX) or xserver (e.g. Step 4: when job is completed, analyze the results. Step 3: submit the system to the local computer cluster Step 2: download the system to local desktop computer Step 1: prepare membrane-OmpLA structure using CHARMM-GUI web-server For info on the cluster see SCS Clusters webpage.

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 TUTORIAL FILES 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.

Vmd tutorial files