I am trying to dock a metalloprotein with a post-translational modification (PTM) to a sequence of DNA, however no experimental evidence exists for the protein-DNA complex as for the atomic/residue interactions that take place.
I essentially want to dock the metalloprotein with PTM and DNA together to perform MD simulations on them, how can I dock these together without defining active/passive residues as I dont know which are active/passive.
I am sorry for the very late reply, but I am trying to implement the solutions provided in the ab-initio tutorial. I am slightly confused by the Noncrystallographic symmetry restraints (NCS). I have the metalloprotein I wish to dock to DNA, so for the NCS segment pairs do I have one pair (A-B)?
Secondly if I have only a single pair, what do I use for segment 1 and 2, do I use the residue numbers 1-41 (A) and segment (B) 1-30 for example?
The NCS option imposes non-crystallographic symmetry restraints: It enforces that two molecules, a fraction thereof or even two sub-domains within the same molecule should be identical without defining any symmetry operation between them
but based in your first response:
You seem to not have any information if its a symmetric complex, in that case you can look into the Best Practices Guide in the section: Information about the interface is not available. For your case it seems that you can try random interactions, surface contacts or center of mass restraints. The links and relevant information are all in the guide, and these options are also accessible via the web interface!
