Desmond Tutorial

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Desmond Tutorial Preparing Proteins with Missing Residues or Side Chains Figure 3.16 Loop comparison: Prime vs. X-ray The green loop is the output of the structure builder. The blue loop is the result of loop refinement. The red loop is the original loop from the X-ray structure. 42 D. E. Shaw Research September 2008
4 Preparing a Desmond simulation with the System Builder Overview The System Builder is a graphical tool in Maestro that lets you generate a solvated system for Desmond simulations. You can launch the System Builder by selecting Applications > Desmond > System Builder from the menu bar as shown in Figure 4.1. Figure 4.1 Launching Desmond System Builder Select Applications > Desmond > System Builder. The System Builder panel appears as shown in Figure 4.2. September 2008 D. E. Shaw Research 43
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Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
Page 5 and 6: from outermost to innermost, separa
Page 7 and 8: Contents Preface . . . . . . . . .
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 53: Preparing Proteins with Missing Res
Page 57 and 58: Preparing a Desmond simulation with
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
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
Page 99 and 100: Analyzing Trajectories Using VMD Lo
Page 101 and 102: Analyzing Trajectories Using VMD Ge
Page 103 and 104: Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD An
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Analyzing Trajectories Using VMD Bi
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10 Documentation Resources Detailed
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Desmond Tutorial

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