Desmond Tutorial

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Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 4.15 Transmembrane hole in the DPPC bilayer for 1su4 Note the large hole within which the protein was inserted. 9. More experienced users may want to run the System Builder job from the command line. Instead of clicking the green Start button, click the Write button to write a command script file to disk that can be executed from the command line. a. Click the Write button in the System Builder window to write the job files to disk. There are two input files: — my_setup.mae. This is the Maestro structure file of the solute (1su4 protein, calcium ions, crystal water molecules, neutralizing ions, and counterions), which serves as the input for system setup. — my_setup.csb. This is the command file, which can be hand‐edited for custom setup cases. For detailed documentation of the .csb file see the Schrödinger Desmond User Manual listed in “Documentation Resources” on page 97. And a single output file (besides a log file): — my_setup-out.cms. This is the Maestro structure file of the entire membrane simulation system including OPLS‐AA force field parameters. For detailed documentation of the .cms file see the Schrödinger Desmond User Manual listed in “Documentation Resources” on page 97. b. Execute the following command at the command line: $ $SCHRODINGER/run $SCHRODINGER/utilities/system_builder my_setup.csb where my_setup is the file name given to “Write”. 56 D. E. Shaw Research September 2008
5 Finishing Preparations for Desmond Simulation Overview There are a few more tasks that must take place before a simulation can be run: • The System Builder will always generate the latest OPLS‐AA force field parameters for the simulation system it builds and the parameters will be included in the .cms output file. However, you may want to assign different force field parameters in case the Schrödinger provided OPLS‐AA parameters are not adequate for a particular system. You can assign alternative force field parameters for your system using a companion program to Desmond called Viparr. • You will also have to specify Desmond run‐time simulation parameters. These topics are addressed in the following sections. Generating Force Field Parameters with Viparr Viparr is a Python script that reads a .cms (or .mae) file and writes another .cms file, which has all the force field parameters required to run a Desmond simulation. Viparr can assign force field parameters from a variety of well‐established force fields and water models. Viparr force field assignment is template based. This means that unlike force field servers, e.g., Schrödingerʹs OPLS‐AA server that can generate parameters for various atom types derived automatically from the moleculeʹs topological structure, Viparr is designed to find templates (such as an entire residue) in .cms files and assign the appropriate force field parameters by looking at a template database associated with a particular force field. The resulting parameters are guaranteed to be identical with those of the published, authentic force field. September 2008 D. E. Shaw Research 57
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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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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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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
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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Desmond Tutorial

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