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
