Hello, I am calculating RNA structures using the 2.16.0 version of XPLOR-NIH. I am using parallhdg.dna as my parameter file. I am having trouble constraining a guanine residue to a syn conformation. Normally one intranuclear restraint (H8 to H1' constrained to 2.15 0.35 0.65) should be sufficient, however this restraint keeps being violated even if that is the only restraint used for that residue (I also have no hydrogen bonding, dihedral angles planarity restraints for that residue) in about half of my structures. Can this be a problem with my parameter file may be something else?
Thank you in advance, Alex Beribisky.
