Desmond Tutorial

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Desmond Tutorial Running Desmond Simulations 68 D. E. Shaw Research September 2008
7 Preparing Free Energy Perturbation Overview You can use Desmond to run free energy perturbation (FEP) calculations using the dual topology approach to perform ligand mutation, annihilation, and single‐atom mutation in a ring. From Maestro, you can visually specify the fixed and variable parts of a molecule that are subjected to FEP calculations and then store the atom correspondence map (which defines dual topologies) in the Maestro .mae file. Ligand mutation—the most common FEP calculation—is illustrated in Figure 7.1 using a typical scenario. The figure shows a graphical representation of the soluble form of the human urokinase plasminogen activator receptor (sUPAR, PDB code 2fd6) and the ZINC‐ 01538934 ligand. The protein structure has been processed using the Protein Preparation Wizard and Prime as described in “Tutorial Steps” on page 3 and “Running Prime” on page 29, respectively, and the ligand was docked using Schrödingerʹs Glide application as part of a virtual screening experiment on the ZINC database (http://zinc.docking.org/). The ligand is rendered in a tube representation in the sUPAR active site with green carbon atoms and ball‐and‐stick representation. September 2008 D. E. Shaw Research 69
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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
Page 29 and 30: Desmond Tutorial Tutorial Steps Fig
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 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: Running Desmond Simulations Running
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
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Page 107 and 108: Analyzing Trajectories Using VMD Bi
Page 109 and 110: 10 Documentation Resources Detailed
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