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.
If you search the forum for zinc you will find the answer…
You need to define specific restraints to maintain the proper zinc coordination
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. Can you please help me provide an example distance restraint file so that I can also setup distance restraints for ion?
Also, is it possible to provide distance restraints using easy interface or will I require higher level (expert or guru) access for that?
As I already told you, the answer is already in the forum… Did you search for it?
Just in case: Zinc finger protein
Yes, I checked in the forum and as mentioned there I have changed CYS to CYF and have submitted the job. But, as also mentioned there that setting unambiguous distance restraint between the ion and cysteine residues could help, thus looking for how to generate these restraint. Currently, also reading your nature protocol paper to see if I can learn from there. Thank You!
In the thread I put in my previous answer there is actually and example of such a distance restraint