Desmond Tutorial

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Desmond Tutorial Preparing Free Energy Perturbation Figure 7.7 Setting FEP parameters from the Run Desmond panel Select ‘FEP’ from the ‘Simulation task’ field. Select the windows that should be included in the simulation. Click the Write button. 2. Select FEP from the Simulation task field. The Simulation section of the panel allows you to set a number of FEP related parameters. For details see the Desmond User Guide and the Schrödinger Desmond User Manual listed in “Documentation Resources” on page 97. 3. Select the λ windows that should be included in FEP simulation. NOTE FEP simulations involve many separate calculations with different values of λ and it is quite possible that some of them will crash at the first try. When this happens, you should rerun the FEP simulation for the failed λ windows. The GUI lets you select the failed λ windows for a re‐run. 4. Write out the Desmond conguration file by clicking the Write button. Running FEP Simulations from the Command Line FEP simulations can be run from the command line using a .cmj file in exactly the same way as described in “Running MultiSim jobs from the Command Line” on page 67: $SCHRODINGER/utilities/multisim -JOBNAME -maxjob -cpu -HOST localhost -host -i .cms -m .msj -o -out.cms 76 D. E. Shaw Research September 2008
Preparing Free Energy Perturbation Adjusting the Conformation of the Mutant NOTE where: • is the name of the job. • is the maximum number of subjobs that can be submitted to a host or a queue simultaneously. A value of zero means that there is no limit. • is the number of CPUs per subjob, which can also be specified as, e.g., ʺ2 2 2ʺ (note the quotes) indicating 8 CPUs with a spatial decomposition of 2x2x2. • -HOST localhost means that the master job runs on your local workstation whereas • given with the -host option is the name of the host or queue where the simulation jobs will be running. To apply non‐default FEP λ parameters, add the ʹ-cfg config_fileʹ option to the command syntax where config_file is a Desmond conguration file. Note that this conguration file will be used throughout the .cmj workflow to make sure that all minimization and MD runs use the same λ settings for consistency. There is a Python script available, which can be used directly to compute the total free energy difference associated with a FEP job. $SCHRODINGER/desmond-v.../bin/ Linux-x86/bennett.py will process the “energy” file output of the different λ runs and compute the free energy. Use the --help option to learn about the use of this script. Adjusting the Conformation of the Mutant The initial conformation of the mutant must be as close as possible to that of the original ligand for FEP simulations. Using Maestro, you can make manual adjustments to the conformation or configuration of small molecules. To show the mutant in its default conformation, click the button in the ʹViewʹ column of the Fragment Library for the fragmentʹs row in the FEP Setup window. In Figure 7.8, the ʹViewʹ option is selected for the butyl fragment. Figure 7.8 Showing a mutant in its default conformation Select the ‘View’ option to show the mutant in its default conformation. September 2008 D. E. Shaw Research 77
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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
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2 Learning the Maestro- Desmond Env
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Learning the Maestro-Desmond Enviro
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Learning the Maestro-Desmond Enviro
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Page 41 and 42: 3 Preparing Proteins with Missing R
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Page 69 and 70: 5 Finishing Preparations for Desmon
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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
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Page 97 and 98: 9 Analyzing Trajectories Using VMD
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