I am a rookie and working on my first NMR structure determination and have to deal with a protein-ligand complex. The protein side is nicely defined with cyana and I have transferred everything over to CNS in order to dock the completely buried ligand (as segid B). I used xplo2d to create both toplogy and parameter files of the ligand (a nucleotide with sugar-ring and base). If I read in a pdb.file of the ligand with protons, it throws them out to create .top and .par file. I really would prefer to have them back in but don't know how. Do I have to use the Hbuild function (I don't know in which interface and where to find/how to run it)?
I tried to run CNS nevertheless without ligand-protons by simply making the NOE distance constraints between protein and ligand looser and to the heteroatom rather than the protons. The output-structures are acceptable but the ligand tends to twist between base and sugar and is not in the right position/orientation. How do I make sure that it doesn't twist? Do I have to change the .top or .par file? What can I do to make hydrogen bonds between protein and ligand energetically more attractive (I don't want to add intermolecular hbonds, because besides gut feeling, I don't have any experimental evidence for them)? Is CNS the best approach for this? Hopefully someone can give me some advice. Thanks for your time, Clemens
