Hello Qinhong-- > > > > > > Does HBDA only work in a limited distance? I have this question because a > > > hydrogen bond pair defined in my HBDA table is always far away (>6A) from > > each > > > other, while it is not reported in violations. Other hydrogen bond pairs > > close > > > from each other are normally reported if violated. So I think maybe the > > software > > > thinks there's no hydrogen bond at all when exceeding certain distance, > > > and > > thus > > > not using that HBDA term? > > > > > > > The HBDA term is not a distance restraint. Rather, it enforces a geometrical > > relationship between the HN-O distance and the O-HN-N angle. A > > distance restraint is also required to keep the atoms close. Please > > see J. Am. Chem. Soc. 124, 10621-10626 (2002). > > Yes, I know HBDA is a distance-angle relation restraint rather than > distance restraint. The problem is there's a pair with N-H...O angle > 107 degree while H...O distance is 7.6A, which is obviously violated > HBDA restraint, but not reported in violations. I think that term > may be not used at all because they are too far away.
There is no distance cutoff in the HBDA term. This is the expression in the hbda code: (1./(RHO**3))-0.019-(0.21/(2.07+ COS(THETA))**3) where RHO is the distance (in angstroms) and THETA the angle in radians. I believe the result is negative, and thus will not be printed in the violation analysis. > By the way, > that hydrogen bond is between protein and ligand, does it matter? If it's in the HDBA restraint table it shouldn't matter. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
