Desmond Tutorial

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<strong>Desmond</strong> <strong>Tutorial</strong> Preparing Proteins with Missing Residues or Side Chains Figure 3.14 Structure Refinement Options window in Prime Select the ‘Serial loop sampling’ option to refine loops separately. Select the ‘Unfreeze side chains within’ option and enter 0.00 in the field to ensure that side chains in the structure do not move. Click OK. NOTE p. Select the Serial loop sampling option to refine loops separately. Serial loop sampling has different levels: default, extended (low, medium, high), and ultra extended. The default option is only recommended for loops up to five residues long. Our loop is a borderline case with 7 residues, but it should be adequate for this exercise. The default mode is reasonably fast: the test case takes only about 15–20 minutes to complete on a single CPU. Even the low‐extended mode would run for much, much longer. q. Enter zero (0.0) in the Unfreeze side chains within field to ensure that side chains in the X‐ray structure do not move. This limits the size of the sphere within which side chains are unfrozen to facilitate better loop conformations by finding good interactions. r. Click OK to store your structure refinement preferences. s. In the Structure Prediction window, click Run under the Refine Structure area. Structure refinement begins. Upon completion, the refined loop appears in the Workspace. As shown in Figure 3.15, the salmon colored structure is the incomplete structure, the green loop is the output of the structure builder, and the blue loop is the result after loop refinement (which has a slightly different conformation). For comparison, Figure 3.16 shows a superposition of all three loops including the original loop from the X‐ray structure in red. 40 D. E. Shaw Research September 2008
Preparing Proteins with Missing Residues or Side Chains Running Prime Figure 3.15 Workspace model after Prime structure refinement The green loop is the output of the structure builder. The blue loop is the result after loop refinement. The incomplete structure has an end that is not connected. t. Close the Structure Prediction window. September 2008 D. E. Shaw Research 41
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 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
Page 51: 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
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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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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