How do I start IFD in the Prime stage with preexisting Glide results?
It can be useful to run a separate Glide job instead of running the initial docking through IFD-for example, if you want to use options not available through IFD, such as addition of metal, hydrophobic, or positional constraints. To use the results of a separate Glide run, use the following procedure: • Be sure to prepare the protein yourself with the Protein Preparation Wizard. (If you are using Schrödinger Suite 2006 you can download this tool as a script from the Script Center . For earlier releases you can use the Protein Preparation panel with Refinement only selected). Also check the protein preparation procedure in the Induced Fit Docking manual and the Protein Preparation Guide. • 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 th
