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Hello Ioannis-- > > 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. > Below is the response I received from Alex Grishaev. Please let us know if this helps. best regards-- Charles Alex> I think the reason is that he did not specify the chain IDs and by Alex> default they are empty, so it does not find anything to work on. I Alex> have a statement below from one of my projects that has HBs between Alex> two segments, he will just have to add "segm" lines. Alex> Alex> Alex> Alex> hbdb Alex> kdir = 0.30 ! directional (3d) dforce const Alex> klin = 0.10 ! linearity (E(ohn|oh) force const Alex> nseg = 2 Alex> nmin = 141 ! min res # to include in the HBDB Alex> nmax = 257 ! max res # to include in the HBDB Alex> segm = C Alex> nmin = 141 ! min res # to include in the HBDB Alex> nmax = 257 ! max res # to include in the HBDB Alex> segm = D Alex> ohcut = 2.60 Alex> coh1cut = 100.0 Alex> coh2cut = 100.0 Alex> ohncut = 100.0 Alex> updfrq = 1000 Alex> prnfrq = 1000 Alex> freemode = 1 ! free mod flag (on) Alex> fixedmode = 0 ! fixed list mode flag (off) Alex> mfdir = 0 Alex> mflin = 0 Alex> kmfd = 0.0 Alex> kmfl = 0.0 Alex> renf = 2.3d0 Alex> kenf = 30.0d0 Alex> @hbdb_files.dat ! location of the PMF files Alex> end Alex> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGjRQGPK2zrJwS/lYRAgkLAJ4yCNIoLhcl1FQ4+76Orj6wIMw4EwCePw6h n1XEAWtF2MmriAlLygScB4U= =Pjmm -----END PGP SIGNATURE-----
