I would like to perform docking of an RNA-protein complex (input 1) to an RNA (input 2). The complex forms 3 bp to my RNA, which I provided as tbl file (Hydrogen bond restraints). I defined the other contacts (protein to RNA) as “active residues”, but the docking results never formed base pairs and the active residues are not even close to each other.
How can I provide more information about the active residues or specialize the contacts?
Thank you so much for your help.