I am trying to use HADDOCK to find the structure of a complex composed of RNA and protein molecules based on restraints collected from NMR spectroscopy. I am using a set of unambiguous intermolecular restraints along with ambiguous restraints both derived from NMR and also based on AIR concept.
I have been quite successful getting the software to run locally starting with known structures of both molecules. However, the results are slightly deviating from the known x-ray structure of a homologous system. Also, I found that the results would be depending on the starting structure of individual molecules, especially the RNA molecule (x-ray structure of a homologous RNA vs. NMR derived structure, both are very similar to each other with RMSD of 2A).
That said, I wanted to try and make Haddock run starting with extended RNA structure and all NMR-derived restraints to guide the structure of RNA molecule. We have experimental restraints that we already used to calculate the RNA model, including unambiguous distances, H-bond basepair info as well as dihedral angles and sugar pucker.
I already tried to use all the aforementioned restraints to dock the complex starting with extended RNA, but that was quite unsuccessful. The calculated complex structure contains the exact same starting RNA structure, even though I kept the whole RNA segment fully flexible. Needless to say that all of my provided distance restraints are violated.
I am wondering if what I am trying to achieve is possible using Haddock2.2? and if I am missing something while setting up my run?
Your help greatly appreciated!