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:
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.
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
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
HETATM11366 ZN ZN+2 724 -8.003 3.205 3.172 0.00 0.00
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.