Step	Problem	Possible Reason	Solution
3	Incorrect protonation of ligand	ADT currently uses Babel to add hydrogen positions, which makes occasional errors	Double-check the PDBQT file and manually curate errors in protonation
4	Missing coordinates in receptor	Experimental coordinate sets are heterogeneous. Common problems include missing side chains and loops, asymmetric units that include only a portion of the biological unit, alternate conformations, essential cofactors and structural waters.	Double-check the PDBQT file and manually curate to include the proper biological unit. In general, use the biological unit and omit ligands and waters except for strongly-bound prosthetic groups.
5(A)iii	Vina does not run	ADT “Start Vina” GUI or command line is not using the proper path to the Vina executable, or file is incorrect CPU or operating system type.	Locate the Vina executable on your computer, and use the appropriate path name. Refer to online installation notes to locate the executable.
5(A)iii	No low energy conformations are found	Grid box does not enclose the active site	Choose an appropriate location for the grid box in ADT
5(B)ii	AutoGrid does not run	ADT “Run AutoGrid” GUI or command line is not using the proper path name to the AutoGrid4 executable, or file is incorrect CPU or operating system type.	Locate the AutoGrid executable on your computer, and use the appropriate path name. Refer to online installation notes to locate the executable.
5(B)v	AutoDock does not run	ADT “Run AutoDock” GUI or command line is not using the proper path name to the AutoDock4 executable, or file is incorrect CPU or operating system type.	Locate the AutoDock executable on your computer, and use the appropriate path name. Refer to online installation notes to locate the executable.
5(B)vi	Re-docking experiments do not reproduce the known pose	System has too many degrees of freedom for AutoDock conformational search	Use longer search protocols, or simplify the system by reducing degrees of freedom (docking in parts or rigidifying part of the ligand)
5(C)i	Problems with selection	Right-click is used in several places in Raccoon for selection – use control-click on Macintosh computers	Use “System Preferences” on Macintosh computers to enable right clicking for the mouse or trackpad,
5(C)vi	No results selected during filtering by interaction	Residue names are case sensitive	Use all capitals, such as THR315
5(D)iv	No low energy conformations are found	Grid box does not enclose all of the side chains	Choose a larger grid box that encloses the binding side and all of the flexible side chains
5(F)iv	Error message about missing W parameters	Water dummy atom parameters not defined in force field parameter file and/or docking parameter files	Ensure that the modified files are used