I have been preparing a .pdb file for docking it has Zinc atoms as part of the complex but there is no charge assigned to them. while docking using HADDOCK requires charge on Zinc atoms, how can I assign charge to atoms? Shall I use any software to do that or edit PDB file itself manually? Suggest software, if any preferable.
Hi Suraj,
I think you can use charge developed from Gaussian View software.
Answer cited from: https://ask.bioexcel.eu/t/c4-zinc-finger-protein/804
"The way to define ions for HADDOCK is explained in Box 3 of our Nature Protocols 2010 server paper: The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897 (2010) https://www.nature.com/articles/nprot.2010.32 . Download the final author version here (link no longer works). In short: the residue name should contain the absolute charge state the atom name should have the exact charge E.g. for a zinc atom: residue name: ZN2 atom name: ZN+2 (atom name with four characters should be shifted by one column to the left)"
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