I am trying to dock a protein with metal ions using the web portal. 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 message:
There was an inconsistency in your data 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
Here are the lines from my PDB that it complains about:
ATOM 943 ZN+2 ZN2 B 300 41.186 -4.686 -1.261 1.00 1.78
ATOM 944 ZN+2 ZN2 B 301 55.503 -5.942 2.967 1.00 2.79
I only have this problem with the web portal. Everything runs fine when I run HADDOCK I have downloaded in Linux and there are no error messages related to Zn2+ ions. If anyone has any advice on what I can do to fix this issue it would be greatly appreciated. Thank you in advance for your help.