Metal ions containing protein

HADDOCK
1

Hi all,
My protein is activated by 5 calcium ions. I made the changes as specified in the protocol. When I submit the protein and its partner for docking I am getting an error message as;

“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 10551 CA+2CA2 A 701 64.184 28.409 -44.098 1.00 64.45 CA”

How can I edit my PDB file suitable for docking?

Many thanks in advance
Sudha

2

Hi there,

As the error message says, you probably have several calcium atoms with the same residue number (701). Try giving each calcium atom a different number.

Also, to check if there are some formatting issues (the PDB format is character-based), have a look at the pdb_format.py tool of pdb-tools