Desmond Tutorial

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Desmond Tutorial Preparing Free Energy Perturbation Figure 7.3 FEP Setup panel for ligand mutation Select the ‘Pick the attachment bond’ option. Select the fragment that will replace the substitution group. Click the Start button. NOTE 2. Select the ʹPick the attachment bondʹ option (the yellow button in Figure 7.3). When you define a structural perturbation for FEP, the ligand molecule is separated into two parts: a fixed part (called the core) and a variable part (called the substitution group). The substitution group will be mutated during simulation, and the core will remain intact. As shown in Figure 7.4, the core and the substitution groups are connected by a single bond termed the attachment bond (green arrow), which has to be picked by hand. Currently, the attachment bond can only be a single, covalent bond in the molecule. When selecting the attachment bond, you determine the direction of the arrow by which half of the attachment bond you select. The attachment bond arrow should point from the core to the substitution group. 72 D. E. Shaw Research September 2008
Preparing Free Energy Perturbation Setting Up an FEP Calculation Figure 7.4 Defining the mutation The attachment bond is shown as a green arrow in the Workspace. The arrow should point from the core to the substitution group. NOTE NOTE 3. Define the mutation to be performed by selecting the fragment(s) that will replace the substitution group from the Fragment Library. For this example, select the butyl row from the list of fragments. The selected row is highlighted in yellow as shown in Figure 7.3. You can apply multiple mutants at a time by using CTRL‐click and SHIFT‐click to select the mutants from the Fragment Library. When you select multiple fragments, FEP simulation creates different systems for each mutant, and runs multiple thermodynamic cycles to compute, respectively, the binding free energy difference between the reference ligand and each of the selected mutants, with respect to the receptor. You can also create arbitrary groups rather than selecting mutations from the Fragment Library. See “Creating a Custom Fragment Group” on page 80 for details. 4. Click the green Start button. FEP simulation starts execution. Desmond uses Bennettʹs acceptance ratio method for FEP calculations, which means that numerous independent simulations will be run for a single FEP calculation. Since the independent simulations can be run simultaneously, you should be careful as to how many simulations can be allowed to run on your host/queue at the same time. You can control this parameter in the green Start window by setting the maximum number of subjobs as shown in Figure 7.5. The value zero means no limit. September 2008 D. E. Shaw Research 73
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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 3.
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Desmond Tutorial Tutorial Steps Sys
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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
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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: 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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