Desmond Tutorial

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Desmond Tutorial Desmond Tutorial Steps to Perform Simulation on a Simple Protein While the example described in this tutorial is a basic simulation on a single protein, the exercise is useful for learning the Maestro‐Desmond environment as well as, in general, investigating the molecular properties of different proteins. Preparing a molecular model for simulation involves these general steps: 1. Import a structure file into Maestro. 2. Prepare the structure file for simulation. During this step, you remove ions and molecules which are artifacts of crystallization, set correct bond orders, add hydrogens, detect disulfide bonds, and fill in missing side chains or whole residues as necessary. 3. Refine the prepared structure file. During this step, you analyze the choices made by Maestroʹs Protein Preparation Wizard and manually change protonation and tautomeric states of variable residues, and (when present) of ligands and co‐factors. 4. If your system is a membrane protein, immerse the protein in the membrane. 5. Generate a solvated system for simulation. 6. Distribute positive or negative counter ions to neutralize the system, and introduce additional ions to set the desired ionic strength (when necessary). 7. Let Maestro assign OPLS‐AA force field parameters to the entire molecular system; alternatively, assign force field parameters external to Maestro with Desmondʹs Viparr utility program, which provides access to a variety of widely used force fields. 8. Configure simulation parameters using the Desmond window in Maestro or edit the Desmond conguration file. 9. Run the simulation from Maestro or from the command line. 10. Analyze your results using the Trajectory Viewer and other analysis tools. This process is illustrated in Figure 1.1. 2 D. E. Shaw Research September 2008
Desmond Tutorial Tutorial Steps Figure 1.1 Simulation process Structure Preparation Input Structure File 1 2 3 Prepare the structure file for simulation. Refine the prepared structure file. Mae Structure File 4 5 Handle ligands or cofactors. Fill in missing residues and side chains. 9 Assign force field parameters to the structure using Maestro or Viparr. 10 Configure DESMOND simulation parameters. 6 7 8 Setup the membrane. Solvate the system. Distribute counter ions. Maeff Structure & Force Field File DESMOND Configuration File Maestro tasks DESMOND-specific tasks 11 Relax/minimize your system and run the Desmond simulation. DESMOND Trajectory File 12 Analyze results. The rest of this section contains step‐by‐step procedures for building and running a simulation of a single protein. Tutorial Steps 1. Start Maestro from your Linux desktop by issuing the following command: $SCHRODINGER/maestro If you access Maestro through the network (e.g., via VNC), start the program by the command: $SCHRODINGER/maestro -SGL This command will launch Maestro using a software OpenGL graphics library. The Maestro window appears as shown in Figure 1.2. If you are unfamiliar with Maestro, see “Learning the Maestro‐Desmond Environment” on page 19. The Schrodinger distribution contains a Maestro Tutorial, User Manual, and Overview that can be consulted for more detailed information. September 2008 D. E. Shaw Research 3
Page 1 and 2: Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
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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: 1 Desmond Tutorial Introducing Desm
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Page 31 and 32: 2 Learning the Maestro- Desmond Env
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Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
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Preparing a Desmond simulation with
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Preparing a Desmond simulation with
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5 Finishing Preparations for Desmon
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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 An
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Analyzing Trajectories Using VMD Bi
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10 Documentation Resources Detailed
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