Hello, I tried to calculate the structures using the nucleic.top/nucleic.par files and unfortunately the problem persists. I have also noticed that in my new coordinate pdb file generated using the nucleic.top/nucleic.par files, the position of the H41 and the H42 atoms is interchanged in some of my cytosine residues. I also went over my script and made sure that the NOE term was indeed on and the force constant is reasonable.
Alex. Quoting John Kuszewski <johnk at mail.nih.gov>: > Hi, > > Step one: Try it again with the nucleic.top/nucleic.par files, since > those are the current ones > (and based on parallhdg.dna, so they're not too different). > > Step two: Take a look at your script. Are you sure you have the NOE > term on? Is the force constant > reasonable? > > > On Feb 20, 2007, at 1:48 PM, yu269821 at yorku.ca wrote: > > > 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. > > _______________________________________________ > > Xplor-nih mailing list > > Xplor-nih at nmr.cit.nih.gov > > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih >
