# Error while protein-ligand docking **URL:** \ **Category:** HADDOCK\ **Created:** [February 24, 2018, 10:21am UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809 "2018-02-24T10:21:44Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Jess2505](https://avatars.discourse-cdn.com/v4/letter/j/977dab/32.png) [@Jess2505](https://ask.bioexcel.eu/u/Jess2505)\ **Post date:** [February 24, 2018, 10:21am UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809/1 "2018-02-24T10:21:44Z")
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: ![Docking](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/66835f464f0bc48362d946942f21f35e5b8aba76.PNG) Thank you so much for your kind help! Best regards Jess ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [February 24, 2018, 10:41am UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809/2 "2018-02-24T10:41:53Z")
Do the residue numbers you define as active exist in the PDBs you are submitting? ---
**Author:** ![Jess2505](https://avatars.discourse-cdn.com/v4/letter/j/977dab/32.png) [@Jess2505](https://ask.bioexcel.eu/u/Jess2505)\ **Post date:** [February 24, 2018, 11:09am UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809/3 "2018-02-24T11:09:04Z")
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. ---
**Author:** ![Jess2505](https://avatars.discourse-cdn.com/v4/letter/j/977dab/32.png) [@Jess2505](https://ask.bioexcel.eu/u/Jess2505)\ **Post date:** [February 24, 2018, 11:48am UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809/4 "2018-02-24T11:48:58Z")
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? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [February 24, 2018, 1:03pm UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809/5 "2018-02-24T13:03:13Z")
Correct! And the additional number officially belong to the PDB format. The first one is the occupancy, the next one the B-factor ---
**Author:** ![Jess2505](https://avatars.discourse-cdn.com/v4/letter/j/977dab/32.png) [@Jess2505](https://ask.bioexcel.eu/u/Jess2505)\ **Post date:** [February 24, 2018, 1:53pm UTC](https://ask.bioexcel.eu/t/error-while-protein-ligand-docking/809/6 "2018-02-24T13:53:02Z")
Thanks for the help! As I started some runs, which use the wrong residue number for the ligand, could you cancel those for me?