Dear all, In a 2 segment protein (seqid a and b) the HBDB potential doesn't find any hbonds in freemode (xplor-nih 2.17) and has correspondingly 0 energy. Single segments work fine. This is similar to posts in the list of about a year ago. Is there any way to get this to work (detecting hbonds within and across the two segments)? I'm pasting here the hbdb parameters used. Thanks in advanced.
John Vakonakis hbdb kdir = 0.20 !force constant for directional term klin = 0.08 !force constant for linear term (ca. Nico's hbda) nseg = 2 ! number of segments that hbdb term is active on nmin = 29 !range of residues (1st) nmax = 134 !range of residues (last) ohcut = 2.60 !cut-off for detection of h-bonds coh1cut = 100.0 !cut-off for c-o-h angle in 3-10 helix coh2cut = 100.0 !cut-off for c-o-h angle for everything else ohncut = 100.0 !cut-off for o-h-n angle updfrq = 10 !update frequency usually 1000 prnfrq = 10 !print frequency usually 1000 freemode = 1 !mode= 1 free search fixedmode = 0 !if you want a fixed list, set fixedmode=1, and freemode=0 mfdir = 0 ! flag that drives HB's to the minimum of the directional potential mflin = 0 ! flag that drives HB's to the minimum of the linearity potential kmfd = 10.0 ! corresp force const kmfl = 10.0 ! corresp force const renf = 2.30 ! forces all found HB's below 2.3 A kenf = 30.0 ! corresponding force const @HBDB:hbdb_files.inp end _______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
