Docking tetrasaccharide to lectin

Hi, I am running some docking experiments on a tetrasaccharide docking to a lectin. The files I submit are 1) receptor/lectin in PDB format, chains A and B, which make up the binding site, 2) tetrasaccharide, in PDB format with HETATM (instead of ATOM) and 4 residues. Both files seem to be processed correctly and the job is submitted. In the results the tetrasaccharide is severed in 4 separate units though, docked separately, as it seems. Not sure what I am doing wrong. Any ideas?

Thank you in advance for your help.

PS. all residues in the tetrasaccharide PDB are labelled as “chain A”, no TER cards in between residues.

Hello Elisa,

HADDOCK is usually building unambiguous restraints to keep the different subunits of a partner together during the docking. This can be the case for multiple chains, as it is the case for you, or when gaps exist in a chain. So you should not encounter any splitting of the subunits during the docking. Can you send me, either by replying to this message, or by email, your job URL? You can also have a look at the unambig.tbl file present in the data/distance directory of your run once downloaded. You’ll know what restraints have been applied to keep the structure together.


Thank you so much Mikael for your quick reply, here is the link to the results,

Not sure if this is the exact URL you’re looking for. As restraints, I specified that all residues, i.e. 1,2,3,4 are involved in the interaction, for the ligand. I also have a number of residues specified in the receptor, i.e. the ones identified through NOE measurements.

Thanks a million!


Actually I did not fully understand the issue at first, sorry for that. But having a look at your job led me to the issue. The 4 molecules you’re trying to dock should be consider as a unique partner with the same residue name. Then HADDOCK will keep them together but there will be still some flexibility allowed if you added some.
If you define 4 ligands, they will behave independently and since HADDOCK does not have a specific protocol to bind more than 1 ligand at the same time, you can get fancy results, as you’ve seen.
So rename all molecule with the same residue name in the PDB of your partner 2 and this should solve this problem.

Hope this will help,


Hi Mikael,

I tried to name the whole molecule as “LIG” residue “1” chain “A” and Haddock doesn’t process the file, saying as an error message “Second pdb file contains multiple residues with number 1 in chain A”.


Hi Elisa

You need to give your tetrasaccharide as a single HETATM residue (i.e. only one residue number) with non-overlapping atom names.

As for your lectin dimer, make sure that there is no overlap in the residue numbering between chain A and B since it will be considered as a single chain in HADDOCK. You will have to adapt your NOE restraints accordingly.

We had a number of CAPRI targets in the past with saccharides and manage to dock up to an octasaccharide following this procedure.


Thank you Alexandre, sounds like a good plan. I did not rename the atoms when I assigned them to residue 1, I just removed the numbers so they were all C N O. I’ll update the post with the results.

Thanks again,

Dear Alexandre and Mikael, the tetrasaccharide, defined as one residue (and one chain) and with distinct atom names is not taken apart and now it all works fine! Thank you so much again for your help!


Hi Elisa and Alexandre,
I am following the exact protocol that you have suggested. However, I am getting the following error:
There was an inconsistency in your data

Error message

Second pdb file contains multiple residues with number 717 in chain C
Directory of the run:|01||385b82ac40234c399afd08d7bf926200|5cdc5b43d7be4caa8173729e3b0a62d9|0|0|637188507772829059&sdata=NjjgIZzJ%2B0ISQenRwGiWFaCspGlzwhPprjmvJfST2t0%3D&reserved=0

can you please have a look?

This means that there are multiple residues with number 717 in chain C of the second molecule, the error message is quite clear.

Thank for your reply,
I have renumbered the residue number to constant value 717 for my polysachharide molecule which has got around 600 atoms, and chainID is constant as well.

I am not sure if I misunderstood the protocol they have discussed here.


Each atom must have a unique name.
You could add a number to the name to distinguish oligosaccharide units

Hi Alexandre,
Thank you so much. I will try according to your suggestion, check if it comes out okay.


Dear Alexandre,
Thank you so much. I have followed your instruction and it is working fine.