Hello Qinhong-- > > I'm calculating a protein with a small molecule ligand. As previous > crystal structure show a critical hydrogen bond between them while > my previous calculation didn' reveal this, I added a tight NOE > (1.5-2.5 A) to pull the Hbond donor and acceptor together. However, > the result structure shows they seem don't quite like each other -- > the hydrogen and oxygen atom stay at the upper limit 2.5 A. They > don't want to get nearer although the crystal structure shows they > can get as close as 1.8 A.
You might first check if the donor/acceptor pairs appear as VDW violations in the .viols file. That would indicate that the nonbonded parameters are preventing them from getting closer. If this is the problem, you can add an NBFIx statement to the parameters to change the nonbonded interaction for only these atoms types. > > I check my script and I'm now wondering whether the electrical term > is included in my potential list, because I don't see a potential > term called elec in my script attached. And I also want to know is > there a list of Xplor potential terms so I can just pick the one I > need? This is used by XplorPot function. Thank you. > Do you think the Coulomb term would help? It is usually not used without solvent. If you really think this will help you might try to refine with explicit solvent, working from eginput/gb1_rdc/wrefine.py. The most comprehensive list of potential terms is probably in the tutorial https://nmr.cit.nih.gov/xplor-nih/doc/current/python/tut.pdf and the old XPLOR manual https://nmr.cit.nih.gov/xplor-nih/doc/current/xplor but, it's probably a good idea to have something in mind before you go hunting. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
