There is a known PDB structure I am using that has solved a NMR structure of a RNA-Protein interaction. I am trying to replicate this ( to test HADDOCK parameters) by submitting just the protein chain as my protein ligand, and submitted a computed 3D structure of the RNA using online folding.
I find that the resulting structure is not identical to the NMR-solved structure and am wondering on how to refine my model further. I know the active residues based on the known structure but right now, I am not designing specific residues as active - I wanted the docking program to compute the residue interaction but I cannot set both the RNA and protein as passive, so I have instead highlighted all RNA and protein residues as active. Is this acceptable, and if not, how would I proceed to theoretically dock my RNA/protein without biasing the model by selecting interactive pairs of residues/nucleotides?