I am using easy interface of HADDOCK 2.4 to dock protein (that contains 3 Zn+2 ions coordinated by 9 cysteines) and DNA. In the resulted best docked model generated, I find that the Zn ions get displaced and no more remains coordinated with cysteines. active residues provided were those that show direct interactions with the DNA. I haven’t included Zn coordinating cysteines in the active residues as these cysteines show no interactions with the DNA. What can be done so that the metal ions (can be restrained) do not get displaced? Will including cysteines in the active residues help (although I find no good reason for that)? Kindly help with your suggestions.