Desmond Tutorial

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Desmond Tutorial Preparing a Desmond simulation with the System Builder tein structure. Click the Preprocess button. The tables will be filled in by the Protein Preparation Wizard. 3. Select the sodium ion in the Het table (the focus of the Workspace view will center and zoom on the Na ion) and then click the Delete Selected button. The sodium ion is just an artifact of the crystallization process, only the Ca ions are integral parts of the protein. 4. You may want to experiment with H‐bond assignment as described in Figure 1.10, but it is not essential for the current membrane setup exercise. Click the Close button to exit from the Protein Preparation Wizard. Figure 4.5 Preprocessing the 1su4 structure Enter ‘1su4’ in the ‘PDB’ field and click the ‘Import’ button. Next, check options in this section as shown. Do not delete the crystal waters. Then click the Preprocess button. Next, select the NA ion and click the ‘Delete Selected’ button. Click the ‘Close’ button. 5. Change the view to ribbon view in the Workspace and orient the protein similar to what can be seen in Figure 4.6, which is the standard way of looking at membrane proteins (with the transmembrane bundle aligned along the vertical axis). 48 D. E. Shaw Research September 2008
Preparing a Desmond simulation with the System Builder Setting Up Membrane Systems Figure 4.6 The 1su4 structure in standard orientation Click the ‘Ribbon’ button... ...and select ‘Show Ribbons for All Residues’ from the popup menu. 6. Launch the System Builder by selecting Applications > Desmond > System Builder. Click the Ions tab and click the Advanced ion placement button. The panel appears as shown in Figure 4.7. Figure 4.7 The advanced ion placement window Click the ‘Select’ button. 7. In this tutorial exercise we do not want to place counterions in the vicinity of the calcium ions. This can be achieved the following way. Click the blue Select button next to the Excluded region field. The selection window pops up as shown in Figure 4.8. September 2008 D. E. Shaw Research 49
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Desmond Tutorial Desmond Version 2.
Page 3 and 4:
Preface Intended Audience This tuto
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from outermost to innermost, separa
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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 55 and 56: 4 Preparing a Desmond simulation wi
Page 57 and 58: Preparing a Desmond simulation with
Page 59: 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
Page 105 and 106: Analyzing Trajectories Using VMD An
Page 107 and 108: Analyzing Trajectories Using VMD Bi
Page 109 and 110: 10 Documentation Resources Detailed
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Desmond Tutorial

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