Disconnected Residues in Non-Relaxed Receptor PDB Output #54
Description
Please find attached a zip archive containing 2 PDB output files of the same receptor protein. These are the non-relaxed and the relaxed versions. The non-relaxed version appears to have disconnected residues or peptides that are interpreted as ligands when the file is opened in Schrodinger Maestro. In contrast, the relaxed version appears not to have chain breaks. Why are there breaks in the non-relaxed PDB file? Is this fragmentation and subsequent defragmentation an integral part of the DynamicBind process? If this is so, then in general, when using the PDB output file of the receptor and the output SDF file of the ligand, should the relaxed forms of each be used? Thank you.