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How do I start IFD in the Prime stage with preexisting Glide results? I want to include Glide options that aren't available from the IFD panel.

If you want to use options that are not available from the Induced Fit Docking panel (such as addition of metal coordination, or positional constraints), you can run a separate Glide job instead of running the initial docking through IFD. To use the results of a separate Glide run with the standard (original) IFD protocol, follow this procedure:

  1. Be sure to prepare the protein yourself with the Protein Preparation Wizard. Also check the protein preparation procedure in the Induced Fit Docking manual and the Protein Preparation Guide.
  2. If you want to mutate receptor side chains to ALA in your Glide job, you need to do it manually. You can use one of the following approaches:

    • Mutate the residues to ALA in the Build panel, and then change the residue name back to the original residue name.
    • Delete all the side chain atoms beyond the CB, and then apply hydrogen treatment to the CB so that it has three hydrogens.
    Both methods produce ALA sidechains while retaining the original residue name, which is required in order for Prime to rebuild the full residue during the optimization stage of IFD.
  3. Run Grid Generation and serial Glide docking jobs with the desired constraints or other options, saving multiple poses per ligand (the IFD default is 20) and applying IFD van der Waals radius scalings (0.5 for the ligand, and 0.7/0.5 for the receptor with/without mutations). You need to run this initial job serially because IFD uses the lignum Glide property to determine which poses were generated from a particular ligand. Running Glide in parallel results in duplicated lignum values, and this would interfere with IFD's ligand and pose tracking.
  4. Set up an IFD job in Maestro as if you were running all stages from the beginning. That is, set job options, put the receptor or complex in the Workspace, define the grid box center, set the Prime refinement and redocking parameters, and so on. You will comment out the Initial Glide docking stage, so the settings for this stage don't matter. For the Ligands to be docked, browse for the ligand file used as input for the Glide job.
  5. Write the job files instead of starting the IFD job, with the Write button.
  6. Edit the jobname.inp file:

    • Comment out the STAGE PPREP section, the STAGE TRIM_SIDECHAINS section and the first STAGE GLIDE_DOCKING section.
    • For the INPUT_FILE (at the top), change the reference from jobname_rec.mae to your glidejob_pv.mae file.
  7. Run the job from the command line:
    $SCHRODINGER/ifd jobname.inp

You can monitor the job's progress in the jobname.log file, or in the Monitor panel. The results are in the structure output file jobname-out.maegz.

Keywords: Maestro

Related Articles:

#867: Is it possible to run IFD with a fixed ligand core, as in Glide docking?

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