Desmond Tutorial

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Desmond Tutorial Desmond Tutorial Figure 1.11 Launching Desmond System Builder Select Applications > Desmond > System Builder. This launches the Desmond System Builder panel shown in Figure 1.12. The System Builder generates a solvated system that includes the solute (protein, protein complex, protein‐ligand complex, protein immersed in a membrane bilayer, etc.) and the solvent water molecules with counter ions. Figure 1.12 Desmond System Builder panel Select ‘SPC’ from the ‘Solvent model’ area. Select ‘Orthorombic’ from the ‘Box shape’ field. Select ‘Buffer’ from the ‘Box size calculation method’ field. Set the distances to 10.0. Check the ‘Show boundary box’ option. Click the Calculate button. 16. Select SPC from the Solvent model field. 17. Select Orthorombic from the Box shape field. 12 D. E. Shaw Research September 2008
Desmond Tutorial Tutorial Steps 18. Select Buffer from the Box size calculation method field. 19. Enter 10.0 in the Distances (Å) field. 20. Check the Show boundary box option and click the Calculate button. The System Builder can also be instructed to minimize the volume of the simulation box by aligning the principal axes of the solute along the box vectors or the diagonal. This can save computational time if the solute is not allowed to rotate in the simulation box. After setting all these options, the Workspace displays the solute and the boundary box as shown in Figure 1.13. Figure 1.13 Solute and boundary box in the Maestro Workspace The solute and boundary box is displayed in the Workspace. 21. Click the Ions tab. The Ions window in the System Builder appears as shown in Figure 1.14. September 2008 D. E. Shaw Research 13
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 21 and 22: Desmond Tutorial Tutorial Steps 11.
Page 23: Desmond Tutorial Tutorial Steps Fig
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 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 73 and 74: Finishing Preparations for Desmond
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Finishing Preparations for Desmond
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6 Running Desmond Simulations Overv
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Running Desmond Simulations Running
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7 Preparing Free Energy Perturbatio
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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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