[Xplor-nih] Ensemble calculation of denatured protein
Jie-rong Huang
jierongh at googlemail.com
Thu Apr 24 10:55:45 EDT 2008
Hi Charles,
Defferent parts of script show different message after showRestraints:
At the begining,
#############
test.py(77): for pre in allPre:
test.py(78): pre.setFreqI(800.)
test.py(81): pre.setEquType("sb")
test.py(82): pre.setAveType("r-6")
test.py(83): pre.setSclType("obsig")
test.py(84): pre.setRlxType("r2dd")
test.py(85): pre.setGammaI(2.713)
test.py(86): pre.setSqn( 0.5 )
test.py(87): pre.setGfac( 2.0 )
test.py(88): print " setting for ", pre.instanceName()
setting for k6c
test.py(89): print pre.showRestraints(0)
0
asignType: normal
--(selection 1)--
C1 2 GLN HN , C2 2 GLN HN , C3 2 GLN HN
--(selection 2)--
C1 6 LYS HN , C2 6 LYS HN , C3 6 LYS HN
obs 1.1967 ( +/- 0.0826 )| calc 0 | diff 0
weight factor : -1.9761
reff : inf
############
############
test.py(412): xpTerms = ["BOND", "ANGL", "IMPR", "VDW", "RAMA", "ORIE",
"PLAN", "NOE", "CDIH", "SANI", "XDIP", "CARB", "COUP", "COLL"]
test.py(413): for xn in xpTerms :
test.py(414): hitemp_potList.add( XplorPot(xn) )
test.py(415): print pre.showRestraints(0)
0
asignType: normal
--(selection 1)--
C1 2 GLN HN , C2 2 GLN HN , C3 2 GLN HN
--(selection 2)--
C1 74 ARG HN , C2 74 ARG HN , C3 74 ARG HN
obs -0.1365 ( +/- 0.0937 )| calc 0 | diff 0
weight factor : -1.9761
reff : inf
#############
There are lots of "VIOLATED" shown after showRestraints after high temp
dynamics
#############
*--- Dynamics ---- step= 500 ---- time= 0.60484 ---- delta_t= 0.0003245
--*
| E(kin)+E(poten)= 100207.732 E(kin)= 4391.636 temperature=
3195.910 |
| E(poten)= 95816.0964056 grad= 36.2284035 ANGL=
14.1780347 |
| BOND= 8.9219472 CARB= 0.0000000 CDIH=
0.0000000 |
| COLL= 11076.4765637 COUP= 0.0000000 IMPR=
1429.0939930 |
| NOE= 0.0000000 ORIE= 0.0000000 PLAN=
0.0000000 |
| RAMA= 695.0249352 SANI= 0.0000000 VDW=
81503.7757233 |
| XDIP= 0.0000000 g35c= 50.4954974 k33c=
163.5663669 |
| k48c= 68.0991698 k63c= 60.8625514 k6c=
158.3771160 |
| r74c= 138.7266213 s20c= 268.8951903 s57c=
179.6026956 |
*------------------------------------------------------------------------------*
test.py(584): ene = s.Epotential()
test.py(585): tmstp = s.stepsize()
test.py(586): ok = checkAndCorrect(s, pene, ene, tmstp, ni,
1000000.0)
test.py(521): badIter = 0
test.py(522): if ene > maxEner :
test.py(525): if ene > pene and ene/pene > 10.0 :
test.py(528): if tmstp < 1.0e-4 :
test.py(542): if badIter == 0 :
test.py(543): command("""
X-PLOR>
X-PLOR> coor copy end ! copy good coordinates
COOR: selected main coordinates copied to comp
X-PLOR>
X-PLOR>end
test.py(546): return 1
test.py(587): ni = ni + 1
test.py(588): pass
test.py(570): while ok == 0 :
test.py(589): return
test.py(778): print pre.showRestraints(0)
0
asignType: normal
--(selection 1)--
C1 2 GLN HN , C2 2 GLN HN , C3 2 GLN HN
--(selection 2)--
C1 74 ARG HN , C2 74 ARG HN , C3 74 ARG HN
obs -0.1365 ( +/- 0.0937 )| calc 6.45264e-07 | diff 0.136501
VIOLATED
weight factor : -4.83089
reff : 120.018
##########
At the step of Cooling, calc is "nan" for all of cases shown:
##########
test.py(865): tempStep = (initTemp-finalTemp)/float(numSteps)
test.py(866): finalTime = 0.2
test.py(867): maxCycle = 100
test.py(868): bathTemp = initTemp;
test.py(869): for i_cool in range(0,numSteps):
test.py(870): print pre.showRestraints(0)
0
asignType: normal
--(selection 1)--
C1 2 GLN HN , C2 2 GLN HN , C3 2 GLN HN
--(selection 2)--
C1 74 ARG HN , C2 74 ARG HN , C3 74 ARG HN
obs -0.1365 ( +/- 0.0937 )| calc nan | diff 0
weight factor : -4.83089
reff : 120.018
S2angular: 0.999956
S2radial: 0.999951
S2: 0.999907
###########
Besides, I didn't set clock atoms in my script, and didn't use proper
spin-label (e.g. assign (resid 28 and name HN) (resid 6 and name OS1)) but
the amide proton of mutated sites. Do they cause problems? Thanks!!!
Best wishes,
Jie-rong
2008/4/23, Charles at schwieters.org <Charles at schwieters.org>:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>
> Hello Jie-rong--
>
> >
>
> > Yes, you are right!I If All PRE related terms are taken out, the script
> can
> > be finished, except: tmsp in checkAndCorrect is too small and I changed
> it
> > from 1.0e-4 to 1.0e-6 to make program go through this error. How can I
> fix
> > the problem about these PREs? Thanks a lot!!
> >
>
>
> I noticed that all of your PRE terms are zero. Perhaps no restraints
> were read in. Please call the method showRestraints(0) for each of these
> terms to make sure the restraints were read in ok. Something like:
>
> print preEs2hn500.showRestraints(0)
>
>
> Charles
>
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