Hello Mandar-- > > I have used anneal.inp with NOEs, Dihe, and hydrogen bond restraints to get a > good ensemble (~ 0.8 A RMSD for ten lowest energy str.). The run is stored > at: > > https://www.dropbox.com/s/0pse0rk3kl6bi6j/run7.tar.gz?dl=0 > > Further, I ran the refine.py with above restraints and RDCs using starting > structure from the lowest energy structure of above (Cartesian dynamics) > calculations. The refined structures are now having an ensemble backbone RMSD > of > ~ 1.2 A. I played with the some the obvious things but ended with no luck. Is > there a way to get lower avg RMSD of the ensemble near to the values given by > anneal.inp? >
I'm not so concerned about having a less precise bundle of structures. Rather, I'm concerned that the quality of the fit of all commons terms appears to be worse. Perhaps the addition of the RDCs is messing things up. You might try a run7 run without RDCs and see how the RMSDs/num violations compares with your initial calculations. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
