It's hard to say for certain without reading your scripts, but are you sure that the square well width (in Hz) that you're using with the potential is less than the tolerance (in Hz) above which you declare a particular Jcoup restraint to be violated?
Also note that even if your violation tolerance is greater than your squarewell width, you can still introduce errors. That's because the forces created by the Jcoup potential depend on the magnitude of the difference between the calculated coupling and the edge of the tolerated region, ie., Jobserved +/- squarewell-width. So if your squarewell width is 0.5 Hz, and a particular restraint is violated by 0.6 Hz, the atomic forces are only 3% of what they would be if you'd used the harmonic potential. So even if though it's violated, that Jcoup restraint is not pushed back into place very hard. Generally speaking, you should keep the Jcoup potential as harmonic. Problems in your structure are far more likely to be caused by mis- assigned NOEs than by 3J couplings. --JK On Aug 14, 2007, at 12:23 PM, Andrew Borgert wrote: > I am running an SA script in vacuum on a small glycopeptide, and I > noticed something strange (to me at least) happen when I changed the > j-coupling potential type. I initially ran my script using a harmonic > potential for the backbone j-coupling ( C-N-CA-C ), however when I > switched to a square potential, the number of j-coupling restraint > violations over the ensemble of structures increased dramatically > (by a > factor of about 2) while the number of violations of other types of > restraints (noe, dihedral, bond, angle etc.) stayed the same. This > seems somewhat counter-intuitive, as switching to a square potential > should be akin to 'loosening' the restraints a bit, which should > result > in fewer violations. Any thoughts? > I realize that my description of the problem is rather vague, so > I'm not > looking for specific trouble shooting, just general advice. > I am running xplor_nih 2.12. > > Thanks > Andrew Borgert > Biophysical Sciences and Medical Physics > University of Minnesota > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
