Why does IFD fail in the initial Glide docking stage?

If multiple entries from the Project Table are included in the Workspace during the IFD setup, each entry is written to the jobname_rec.mae file as a separate receptor. Unfortunately, if the ligand and receptor used to set up the job were distinct included entries, the ligand is treated as a separate "receptor" instead of part of a ligand-receptor complex that must be extracted the during initial Glide docking stage. This causes failures in the initial Glide stage.

This is likely to be the problem if the jobname.log file reports that the "Number of initial structures" is more than one. The initial docking stage prints a warning about missing _pv.mae files and the IFD job stops. Error messages indicative of this problem are a "ZeroDivisionError: float division" message in the jobname_rec-N_*.log file or errors reading the receptor structure in the jobname_rec-N_*_grid.out or jobname_rec-N_*_dock.out files.

To avoid this problem, merge the ligand and receptor into single entry in the Project Table, and include only that new entry in the Workspace when setting up the IFD job.

Keywords: Induced fit docking, multiple structures

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