Desmond Tutorial

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Desmond Tutorial Learning the Maestro-Desmond Environment Figure 2.3 Sequence Viewer The Sequence Viewer appears at the bottom of the window when you select Display > Sequence Viewer from the menu bar. Changing Selection Mode in Maestro You can change the selection mode within the workspace to allow selections based on atom, residue, molecule, and so on. To quickly switch selection mode, click and hold the Workplace selection button located in the upper left corner of the main toolbar as shown in Figure 2.4. New options appear allowing you to change selection mode. The letter on the Select button indicates the current selection mode. Figure 2.4 Selecting mode display Click the ‘Workplace selection’ button to change the selection Maestro also offers a powerful tool for selecting arbitrary sets of atoms—the Atom Selection Tool. To open the Atom Selection dialog box, choose the Select option from the Workplace selection button. From the Atom Selection dialog box you can make complex 22 D. E. Shaw Research September 2008
Learning the Maestro-Desmond Environment Editing a Molecular Structure selections on the different tabs of the tool, including SMARTS. Configurations within the Atom Selection dialog box are translated to an ASL (atom specification language) expression. The settings shown in the Atom Selection dialog box in Figure 2.5 constrain the workspace to show residues that are at least 5 Å away from the backbone of polar residues. Figure 2.5 Atom Selection dialog box Select arbitrary sets of atoms from the tabs of this window to show the desired residues in the Workspace. Editing a Molecular Structure Maestro provides a general structure building and editing tool. It can be accessed either from the main toolbar by clicking the `Hammerʹ button as shown in Figure 2.6, or by selecting different editing tools from the Edit menu. When you click the `Hammerʹ button, the most common editing options appear as icons in the top horizontal toolbar. These tools allow you to hand‐draw structures, set chemical elements, increment/decrement bond order or formal charge, adjust the position of atoms, clean up 3D geometry, and add common molecular fragments. View help for each toolbar icon by slowly moving the cursor over the icons. Figure 2.6 Opening the Build/Edit Icon Menu General tools for building and editing molecular structures appear when you click the ‘Hammer’ button. As shown in Figure 2.7, the Build/Edit menu includes: • Fragments for adding molecular fragments to your structure. September 2008 D. E. Shaw Research 23
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: Learning the Maestro-Desmond Enviro
Page 37 and 38: Learning the Maestro-Desmond Enviro
Page 39 and 40: 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 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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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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