Dear Dr. Bonvin and coworkers,
I have just recently started using Haddock and I am getting the same error message over and over again:
TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO!
CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS
STRUCTURE NUMBER 51
(The number is changing each time I do a new calculation, so I have no idea what it could mean.)
I have already checked the pdb files of my proteins and the ligands and I can’t find the problem for it.
Maybe you can see from my input in the easy/prediction interface what I am doing wrong:
Thank you so much for your kind help!
Do the residue numbers you define as active exist in the PDBs you are submitting?
Yes, for the protein, I have checked in pymol that those residues are included in the pdb file.
For the ligand, I am not sure what to enter as the ligand is a small molecule and does not have “residues” as the protein does. My supervisor told me to enter “1” here.
I think I have just realized where to find this “residue number”, but just to check:
If the pdb file of my ligand says:
HETATM 1 O1 UNK 900 5.031 0.150 0.718 1.00 0.00 O
then “900” is the “residue number” which to enter.
If it looks like this instead:
HETATM 1 H 1 -0.416 -2.345 0.631 H
then “1” would be the correct residue number.
Is that correct?
Also, there are additional numbers added in the first case (1.00 0.00). Does Haddock require these or will a pdb file lacking these values (like the second case) also work?
And the additional number officially belong to the PDB format. The first one is the occupancy, the next one the B-factor
Thanks for the help!
As I started some runs, which use the wrong residue number for the ligand, could you cancel those for me?