Hi Yuan, The threshold energy associated with a particular term of torsionDBPot represents an isoenergetic surface that envelopes most of the database points used to generate the term. Following your example, 99.95% of the Lys (chi1, chi2, chi3) data points have an energy of 20.955 or lower. Your violations are just telling you that you have a few Lys (chi1, chi2, chi3) angles outside the region where 99.95% of our database points live.
If your experimental restraints (NOEs, etc.) support a conformation that "violates" torsionDBPot, then you should trust your experimental data. In other words, experiments take precedence over torsionDBPot. Thus, violations of torsionDBPot are less serious than, say, NOE violations. I wouldn't increase the force constant of torsionDBPot because you run the risk of overweighting it relative to your experimental restraints. Bottom line: you shouldn't be too concerned about your torsionDBPot violations, particularly if you have just a few. With regards to your deviations of covalent geometry, they might be caused by differences in the CNS and Xplor-NIH forcefields. If you want to fix them, before you start with your Xplor-NIH refinement, you could try running the function fixupCovalentGeom(): import protocol protocol.fixupCovalentGeom() I hope this helps. Best, Guillermo ________________________________________ From: Yuan Yang [[email protected]] Sent: Friday, February 13, 2015 2:53 PM To: [email protected] Subject: [Xplor-nih] Torsion DB Pot violations and deviation from ideal geometry Hi all! I keep getting a few torsionDBPot violations, which does not go away if I increase the torsionDBPot force constants twice from the eginput/gb1_rdc/refine.py values. I also tried changing the force constants of other potentials (noe, dihedral, hbond, vdw) one by one, which did not seem to change anything about the torsionDBPot violations either. I wonder what parameter(s) is related to this subject? And what kind of torsionDBPot violation is considered acceptable? For example in most structures of my ensemble, I get an Energy of 21.024 for a Lys_chi1_chi2_chi3, while the Threshold energy is 20.955. Is this a serious violation? On the other hand, I am refining an NMR structure, in which I input NOE restraints assigned by ARIA2.3/CNS1.21. I am consistently getting twice larger deviations from ideal geometry for both bond angles and bond lengths in Xplor ensemble as compared to ARIA ensemble. These deviations do not seem to depend on any of the force constants, SA parameters, or water refinement. I wonder if this is originated from the intrinsic differences between torsion angle dynamics (used in Xplor) and Cartesian space dynamics (used in ARIA)? Thanks very much in advance for comments and suggestions! Best regards, Yuan Yang Graduate Student Department of Biochemistry & Biophysics Texas A&M University _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
