Hi Ning-- > Thank you so much for the answer to the EEFx parameters between > different xplor-nih versions. > In my mind, the total energy mainly depends on the tDB and EEFx > energy, the total energy will become less if the EEFx energy is more > negative. Do you know the acceptable range of EEFx energy for > high-quality NMR structure?
The EEFx energy (which includes Van der Waal, electrostatic and solvation components) doesn't represent a quality metric. You should look at the number of nonbonded clashes, percentage of buried hydrophobic residues and the like- outside of Xplor-NIH's metrics. If there are problems, these will usually to accompanied by violations in bond, angle and improper violations, in addition to violations of your experimental restraints. The TorsionDB term also reports violations, corresponding to combinations of torsion angles which are very unlikely given the values seen in high quality crystal structures. > Can you please give me some suggestions > about how to decrease the energy of tDB and EEFx? > If your experimental restraints are satisfied, please run molprobity, the wwPDB's validation server or a similar program to see what those programs think of your structure. If you have a largely unstructured protein, a different approach will be required. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
