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
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