Desmond Tutorial

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Desmond Tutorial Preparing Free Energy Perturbation Figure 7.11 Ugly contacts removed Bad contacts are the only contacts that remain. The Ugly contacts have been removed. Creating a Custom Fragment Group If the Fragment Library does not have the mutant structure you want to use, you can edit any pre‐defined substitution group manually using the Build/Edit tools. The only caveat is that the customized substitution group will retain the name of the fragment that you modified. However, the FEP simulation will use the modified fragment. 80 D. E. Shaw Research September 2008
8 Visualization and Analysis using Maestro Overview Maestro provides two basic visualization and analysis tools. Maestroʹs Trajectory Player is similar to the ePlayer found in the Project Table, which was mentioned in “Maestro Projects” on page 24, but it is specifically designed to nicely animate Desmond trajectories much faster than the ePlayer could, and it has a number of specific visualization options. Maestro can also perform basic quality analysis using the Simulation Quality Analysis window. The following sections cover the basics of these tools. Animating Desmond Trajectories with the Trajectory Player Assuming that you have completed the first exercise in this tutorial in “Tutorial Steps” on page 3 you should have a completed Desmond simulation of the 4pti structure in your working directory with the base name of desmond_job by default (unless you gave it a different name). 1. Select Project > Import Structures: Read in the desmond_job-out.cms file. You will have to set the file format selector in the Import panel to CMS to display .cms files in the file browser window. 2. Select Project > Show Table: Open the Project Table. The Trajectory Player can be launched from the Project Table. Note the blue T button in the Aux column in the Project Table, as shown in Figure 8.1. September 2008 D. E. Shaw Research 81
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Desmond Tutorial Desmond Version 2.
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Preface Intended Audience This tuto
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from outermost to innermost, separa
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Contents Preface . . . . . . . . .
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Loading Files from the Command Line
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List of Figures Figure 1.1: Simulat
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1 Desmond Tutorial Introducing Desm
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Desmond Tutorial Tutorial Steps Fig
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Desmond Tutorial Tutorial Steps 3.
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Desmond Tutorial Tutorial Steps Sys
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2 Learning the Maestro- Desmond Env
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Learning the Maestro-Desmond Enviro
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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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Page 69 and 70: 5 Finishing Preparations for Desmon
Page 71 and 72: Finishing Preparations for Desmond
Page 77 and 78: 6 Running Desmond Simulations Overv
Page 79 and 80: Running Desmond Simulations Running
Page 81 and 82: 7 Preparing Free Energy Perturbatio
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Page 97 and 98: 9 Analyzing Trajectories Using VMD
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Desmond Tutorial

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