[Xplor-nih] HBDB and segments

[Charles at Schwieters.org]

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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> 
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