Dear all,
I was trying to dock a metalloprotein (Zn2+) with peptide using the web https://milou.science.uu.nl/services/HADDOCK2.2/haddockserver-prediction.html. I followed the instructions in the HADDOCK Nature Protocol paper for naming as well as advice from previous discussion topics but I am still getting the following error messages:
Error message
Unable to generate topology for ligand ZN+. PRODRG did not create the required output:
PRODRG> Found unsupported atom type Z (atom ’ ZN ') in your coordinates.
Error message
First pdb file contains an unknown amino acid or nucleic acid base ZN2
Make sure to use three letter code for bases and amino acid
Error message
First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble
ATOM 11366 ZN ZN+2 724 -8.003 3.205 3.172 0.00 0.00
I have tried:
HETATM11366 ZN ZN2 724 -8.003 3.205 3.172 0.00 0.00
END
HETATM11366 ZN ZN+2 724 -8.003 3.205 3.172 0.00 0.00
END
HETATM 7003 ZN+2ZN2 724 -8.003 3.205 3.172 0.00 0.00 ZN2
Any help would be highly appreciated. Thanks in advance.
If anyone has any advice on what I can do to fix this issue it would be appreciated.
Best regards,
M.
1 Like
Unable to generate topology for ligand ZN+. PRODRG did not create the required output:
Found unsupported atom type Z (atom ’ ZN ') in your coordinates.
This nomenclature does not follow the instructions since the atom name should be ZN+2 and the residue name ZN2
Be careful with the columns in your PDB file!
The ZN+2 atom name should be shifted by one column to the left (i.e. there should be a space between the atom and residue names).
First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble
ATOM 11366 ZN ZN+2 724 -8.003 3.205 3.172 0.00 0.00
And if you have multiple zinc atoms, each should have unique residue and atom numbers
Thank You. 
I’ll try that in a sec. This:
ATOM 11364 O TRP 723 14.358 -11.928 -18.565 0.00 0.00
HETATM11366 ZN ZN+2 724 -8.003 3.205 3.172 0.00 0.00
END ?
Tnx.
Best regards,
M.
This is not following the instructions in our Nature Protocol paper…
In the PDB format, the atom name comes before the residue name. Now you swapped those.
AND the residue name must be ZN2 instead of ZN
Almost there!
Thank You so much… Yeah, You are right… but I got so desperate that I had no idea what I writte… 
This works so I’ll post a pic for those with same problems like me. Thank You!!! 
THIS IS IT:
Best regards,
M.
1 Like