Using Zn2 as a ligand


#1

Dear Prof.Bonvin and coworkers
I am interested in study protein-Zn interaction using HADDOCK server: the Easy interface. I use this file as a PDB for Zn.
HETATM 1 ZN+2 ZN2 1 1.603 11.925 27.136 0.50 31.56 ZN
END
However I received an email with the following error:
“There was an inconsistency in your data
Error message
First pdb file is incorrectly formatted. Please align the columns of your PDB properly.”

I tried to do it some times but it doens’t work. Would you help me to fix this file or suggest me what should I do, please?,
Thanks you


#2

To check if there are some formatting issues (the PDB format is character-based), you can use pdb_format.py from our set of pdb-tools


#3

The PDB format is quite strict with spacing and it’s very easy to make mistakes editing it manually. As Adrien suggested, have a look at our pdb-tools. We just released a new version and some tools changed name: pdb_validate is now the tool to check where a structure is badly formatted.


#4

The problem was resolved using the pdb-tools.
Thanks you very much.