Dear Charles, Thanks for your suggestions.
I am seeing issues only when I run python scripts (anneal.py or refine.py). Same restraints give me a nice bundle with anneal.inp but if I move to .py then I end up messing RMSD by 0.3-0.4 A. I already checked .py scripts with and without RDCs and they do not make much difference. BTW, I also played with weighing RDCs which did not make any significant difference. Please let me know, Mandar > On 04-Nov-2014, at 12:02 am, Charles Schwieters <[email protected]> > wrote: > > > 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
