Download Desmond Quick Start Guide

Contents
Document Conventions ...................................................................................................... v
Chapter 1: Introduction ....................................................................................................... 1
1.1 Tutorial Outline .......................................................................................................... 1
1.2 Creating a Working Directory .................................................................................. 2
1.3 Starting Maestro ........................................................................................................ 2
Chapter 2: Preparing Proteins ....................................................................................... 3
2.1 Preparing 1bel ............................................................................................................ 3
2.2 Preparing 2qdz ........................................................................................................... 5
Chapter 3: Building a Model System ........................................................................ 7
3.1 Building a Model System for Butane ..................................................................... 7
3.2 Building Model Systems for 1bel ........................................................................... 8
3.3 Building a Model System for 2qdz ....................................................................... 11
Chapter 4: Molecular Dynamics Simulations .................................................... 17
4.1 MD Simulations for Butane .................................................................................... 17
4.1.1 Running the Simulation..................................................................................... 17
4.1.2 Viewing the Trajectory....................................................................................... 19
4.2 MD Simulations for 1bel ......................................................................................... 21
4.2.1 Running the Simulations ................................................................................... 21
4.2.2 Setting Up the Display....................................................................................... 22
4.2.3 Viewing the Trajectory....................................................................................... 24
Getting Help ............................................................................................................................. 27
Desmond 2.2 Quick Start Guide
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