I get very high Reference RMSD values in my DLG; what went wrong?Up to table of contents
This FAQ applies to: AutoDock 3, AutoDock 4
The "Reference RMSD" values that are printed in the "RMSD TABLE" in the DLG are computed from the coordinates of
- either the input ligand (PDBQ or PDBQT) file specified by the "move" command in the DPF, if you did not include the "rmsref" command in your DPF;
- or the ligand (PDBQ or PDBQT) file you specified in the "rmsref" command in the DPF.
If you do not specify the "rmsref" command, and the ligand input coordinates happen to be translated far from the receptor, you will appear to get high Reference RMSD values. _Don't Panic!_ This is normal, and you don't need to worry about these high values.
You may want to check that the input ligand coordinates are far from the crystallographically observed binding position in active site, by reading in the input ligand and the receptor in ADT.
We usually use the "rmsref" DPF-command to specify the x-ray crystallographic coordinates of a known binding mode taken from a complex PDB structure. This can be a useful way of checking if your redocking is successful, if the Reference RMSD values are less than 2-3 Å from the crystal structure position of the ligand.