Desmond Tutorial

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Desmond User’s Guide iv D. E. Shaw Research September 2008
Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .i Intended Audience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i About this Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii Format Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii About the equations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii 1. Desmond Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Introducing Desmond . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Steps to Perform Simulation on a Simple Protein . . . . . . . . . . . . . . . . . . . . . 2 Tutorial Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2. Learning the Maestro-Desmond Environment . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Zooming In and Restoring Full View. . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Visually Distinguishing Residues and Displaying Atom Information . . . . . . . . 21 Changing Selection Mode in Maestro . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Editing a Molecular Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Maestro Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Useful Tools in Maestro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3. Preparing Proteins with Missing Residues or Side Chains . . . . . . . . . . . . . . . . 29 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Running Prime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 September 2008 D. E. Shaw Research v
Page 1 and 2: Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
Page 5: from outermost to innermost, separa
Page 9 and 10: Loading Files from the Command Line
Page 11 and 12: List of Figures Figure 1.1: Simulat
Page 13 and 14: 1 Desmond Tutorial Introducing Desm
Page 15 and 16: Desmond Tutorial Tutorial Steps Fig
Page 17 and 18: Desmond Tutorial Tutorial Steps 3.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
Page 31 and 32: 2 Learning the Maestro- Desmond Env
Page 33 and 34: Learning the Maestro-Desmond Enviro
Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
Page 55 and 56: 4 Preparing a Desmond simulation wi
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Preparing a Desmond simulation with
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5 Finishing Preparations for Desmon
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Finishing Preparations for Desmond
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6 Running Desmond Simulations Overv
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Running Desmond Simulations Running
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7 Preparing Free Energy Perturbatio
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Preparing Free Energy Perturbation
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8 Visualization and Analysis using
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9 Analyzing Trajectories Using VMD
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10 Documentation Resources Detailed
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