Desmond Tutorial

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<strong>Desmond</strong> <strong>Tutorial</strong> Preparing Free Energy Perturbation Now click Maestroʹs Adjustment tool on the left icon menu as shown in Figure 7.9 to turn on the manual adjustment option. You can click this button to switch between manual adjustment mode and global translation/rotation mode. Figure 7.9 Manual adjustment of the substitution group conformation Click the ‘Adjustment’ button to enable manual adjustments, such as “quick-torsion”. Click the attachment bond (shown in green) to display the non‐bonded contacts between the butyl fragment and the ligand core. As shown in Figure 7.10, there are bad contacts (displayed in orange) and ugly contacts (displayed in red). Good contacts are not shown by default because there are too many of them. See the documentation on the Measurements panel for the Contacts tab. Removing the ugly contacts is a good idea, and the bad contacts remaining are probably not a big issue. 78 D. E. Shaw Research September 2008
Preparing Free Energy Perturbation Adjusting the Conformation of the Mutant Figure 7.10 Displaying the non-bonded contacts Bad contacts are shown in orange. Ugly contacts are shown in red. To arrive at a suitable conformation of the substitution group, you must adjust the torsion angle (and often, multiple angles). You can alter the torsion angle manually by holding down the left mouse button and moving the mouse horizontally, or by rotating the mouse wheel. For our example, the attachment bond was rotated 120 degrees to remove bad contacts. As shown in Figure 7.11, the altered butyl conformation is now fairly close to that of the original –N+H 2 — CH 2 — N+H 2 —CH 3 group. To restore the default conformation, you can click the button in the ʹResetʹ column in the FEP Setup panel. September 2008 D. E. Shaw Research 79
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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 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 39 and 40: 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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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
Page 83 and 84: Preparing Free Energy Perturbation
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Page 93 and 94: 8 Visualization and Analysis using
Page 95 and 96: Visualization and Analysis using Ma
Page 97 and 98: 9 Analyzing Trajectories Using VMD
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Page 109 and 110: 10 Documentation Resources Detailed
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