How do I start IFD in the Prime stage with Glide results from a separate Glide docking job? I want to access additional functionality (e.g., metal/hydrophobic/positional constraints) or modify Glide parameters that aren't configurable through the IFD interface.

First, since you won't be running the "Protein Prep constrained refinement" stage of IFD, be sure to prepare the protein yourself, in the Protein Preparation Wizard.

If you want to mutate receptor side chains to ALA in your Glide job (as you would do in IFD), you need to do it manually. Either 1) mutate the residues to ALA with the Build panel, and then change the residue name back to the original residue name, or 2) delete all the side chain atoms beyond the CB, and then add hydrogens to the CB so it has three hydrogens. Both methods will produce ALA side chains while retaining the original residue name, which is required in order for Prime to rebuild the full residue during the optimization stage of IFD.

Next, 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 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/pose tracking.

Set up an IFD job in Maestro as if you were running all stages from the beginning. You will be commenting out the "Initial Glide docking" stage later, 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 that you just ran.

Click Write to write the job files instead of starting the IFD job.

Edit the jobname.inp file and 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 of the .inp file), change the reference from 'jobname_rec.mae' to the pose-viewer output file from your Glide job, glidejob_pv.mae file.

Finally, run the job from the command line:

$SCHRODINGER/ifd jobname.inp

Keywords: IFD, Prime stage, previous Glide results

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