Desmond Tutorial

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<strong>Desmond</strong> <strong>Tutorial</strong> Preparing Proteins with Missing Residues or Side Chains To run Prime: 1. Download the 1su4 structure as shown in Figure 1.4 on page 5. This structure has all residues present in the PDB file, but as a working example, we will delete a small loop by hand‐editing the PDB file. 2. Delete residues 132–136 from the 1su4 PDB file by hand (the original PDB file should be in the working directory after the download) and save it as 1su4_missing_loop.pdb. 3. Import the modied PDB structure into Maestro as shown on Figure 1.3 on page 4. The truncated structure replaces the full structure in the Workspace where the missing loop is called out in a red box in Figure 3.1. Figure 3.1 Missing loop in the 1su4 protein The loop between the two orange ribbons is missing. The white gaps in the residues (shown in green) represents the missing loop. NOTE NOTE 4. Apply Prime to the truncated 1su4 protein structure with the missing loop. Running Prime can be computationally intensive. To save time, you can distribute Prime jobs among multiple CPUs. If your protein only has missing side chains (no missing residues), you can select the Predict side chains task under Applications > Prime > Refinement to automatically fill in the missing residues without running the entire Prime structure prediction protocol as shown in Figure 3.2. 30 D. E. Shaw Research September 2008
Preparing Proteins with Missing Residues or Side Chains Running Prime Figure 3.2 Automatic side chain prediction in Prime Select ‘Predict side chains’ from the ‘Task’ field to automatically fill in missing side chains. a. Select Applications > Prime > Structure Prediction from the menu bar. The Structure Prediction window appears as shown in Figure 3.3. Figure 3.3 Prime Structure Prediction window Click ‘From File...’ to input a sequence from a file. b. Click From File under Input Sequence. The Input Sequence From File window appears as shown in Figure 3.4. September 2008 D. E. Shaw Research 31
Page 1 and 2: 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: 3 Preparing Proteins with Missing R
Page 45 and 46: 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 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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8 Visualization and Analysis using
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Visualization and Analysis using Ma
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9 Analyzing Trajectories Using VMD
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Analyzing Trajectories Using VMD Lo
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Analyzing Trajectories Using VMD Ge
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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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