What does it mean if the docking stage fails with an error about atom overlaps in the structure file?
If the failure is in the redocking stage, it is likely that Prime has placed some hydrogens badly. This can happen if the input file has bad hydrogen atom names, such as mixed remediated and unremediated names. The problem can usually be fixed by deleting all hydrogens and applying a hydrogen treatment prior to running IFD. If the initial docking is failing, it is likely that the input structure has an overlap. This should not be the case if the Protein Preparation constrained refinement was run. It is also possible for the side-chain removal (mutation) procedure to yield bad structures if the PDB atom names of the residues are incorrect. There is also a known issue in the original Suite 2008 Prime release (verison 20110) that causes LYN residues to be assigned bad hydrogen names in Prime refinement output files. A subsequent Prime calculation places these LYN hydrogens in overlapping positions. This issue can cause an overlap error within IFD itself if the job is running two Prime sta
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