Dear all,
I am trying to use the HBDB potential using a customized version of
the "~/eginput/gb1_rdc/refine.py" xplor-nih python script.
I define the HBDB parameters using the xplor.command('...') syntax
after reading psf and pdb-coordinates.
I add the HBDB potential to the potentail list by the command:
potList.append(XplorPot('HBDB'))
However, the HBDB potential doesn't find any hbonds in freemode
"# of active HBDB terms : 0"
(xplor-nih 2.18).
What is wrong, is it possible to use HBDB from the python interface?
Below is the HBDB context from my python script:
-----------------------------------------
protocol.initStruct("xxx.psf")
protocol.initCoords('xxx.pdb')
from potList import PotList
potList = PotList()
from simulationTools import MultRamp, StaticRamp, InitialParams
rampedParams=[]
highTempParams=[]
#setup HBDB term
xplor.command('''
!hb database must be read in after psf file
hbdb
kdir = 0.20 !force constant for directional term
klin = 0.08 !force constant for linear term (ca. Nico's hbda)
nseg = 1 ! number of segments that hbdb term is active on
nmin = 1 !range of residues (1st)
nmax = 70 !range of residues (last)
!segm = A !uncommenting has no effect
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
''')
from xplorPot import XplorPot
potList.append( XplorPot('HBDB') )
----------------------------------------------------
Hope you can help me,
best Regards,
Jakob
Citat af Ioannis Vakonakis <ioannis.vakonakis at bioch.ox.ac.uk>:
> 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
> Xplor-nih at nmr.cit.nih.gov
> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
>
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