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Article ID: 82 - Last Modified: May 4, 2011

I would like to add restraints to my relative FEP calculation. How can I do that?

Adding restraints will bias your simulation results, and is only valid if you believe the effects of the restraints will cancel. To add the restraints, follow these instructions:

  1. Set up the job from the Maestro panel, but use the Write button to write out the files instead of starting the job.
  2. Make a backup copy of the jobname.msj file.
  3. Edit the .msj file so that it contains only the first two stages (i.e. the "task" and "system_builder" stages).
  4. Execute the job from the command line using the command from the bottom of the .msj file. This should be fast, and produce a -out.cms file.
  5. Read this -out.cms file into Applications → Desmond → FEP. Go to Advanced Options → Restraints and add your positional restraints. Save your changes, and write out the files.
  6. Use only the .cms file from step 5 with the original (i.e. backed up) copy of the .msj file from step 2, except remove the "system_builder" task from the file, since you already performed that step. You can then launch the job from the command line.

Keywords: FEP restraints

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