I used “get-dockings” to extract the docked conformations. Where is the macromolecule?
After you extract the docked conformations from the AutoDock log file using get-dockings, you obtain a PDB formatted file that contains the docked conformations of the ligand. These are sorted in order of increasing energy, and in accordance with the conformational clustering. This PDB file puts each docked conformation in between MODEL and ENDMDL records. This file does not contain the macromolecule coordinates which you docked to. Don’t Panic! These are still in the original PDBQS file you used to generate the AutoGrid maps. In other words, the output docked coordinates of the ligand are written in the same reference frame as the original macromolecule PDBQS. To view the dockings in relation to the macromolecule, in InsightII 2000, for example, read in the PDB file of MODELs first (with “Keep all frames” turned on). Then read in the macromolecule PDBQS file using the first docked conformation as the “Reference” structure. You can read in the PDBQS file as a PDB formatted file (it wor
