What can I do if IFD dies in the Protein Preparation stage? There is a warning:

Expected output file _rec-1_ref.mae not found.

and the jobname_rec-1.log file in the jobname_workdir/ directory has this message:

** Final rmsd is greater than 0.18. No output structure is saved.
Increase the rmsd limit via [-r rmsd] and run refinement again.

This error means the structure moved too much (>0.18 Å RMSD) during the first step of the "Protein preparation constrained refinement". This stage of the IFD workflow can be skipped if you've already prepared your system with the Protein Preparation Wizard (which we recommend using).

If you want to relax the receptor within IFD itself, and 0.18 is too strict an RMSD cutoff, you can increase it to, say, 0.30 by changing the RMSD parameter in the "STAGE PPREP" of the jobname.inp file and then running the job from the command line:

$SCHRODINGER/ifd jobname.inp

One possible cause of the 0.18 Å cutoff being insufficient to relax the structure is an input receptor structure that includes significant clashes. This could be a sign that the input model quality is not high. We recommend using the full Protein Preparation Wizard treatment to prepare the receptor, as this will provide more opportunity to examine and refine the structure prior to using it in simulations.

Keywords: protein preparation, IFD, RMSD, cutoff

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