Hi all. I have been attempting to dock a dimeric protein to single stranded DNA. I have assigned the entire DNA molecule as flexible but I see no conformation changes between the input PDB and the modeling output. I am using the webserver and the DNA was created simply using the FNAB command in PyMol and editing the HETATM tags in the text file. Any advice on why my molecule is showing no flexibility? I fed no restraints, and instead am using ambiguous docking.
Did you define the DNA as fully flexible?
And without specific restraints, I would not expect any significant conformational changes… Did you turn on the center of mass restraints? Or what do you mean by “using ambiguous docking”?
I can send param file if it’d be helpful, but essentially we have assigned the surface of our dimeric protein as automatically passive, and the DNA has been assigned ten active nucleotides at the center of its sequence. The entire DNA molecule was marked as fully flexible.
Did you also define your DNA as fully flexible?
Can you share a link to a run (if you have used the server)?
You can also sent it by email.