Dear Charles,
Thank you very much for your reply. I am not sure if I understand you
correctly. Do you mean the final temperature of cooling should be room
temperature (e.g. 298K) instead of 25K in the script? And the high
temperature dynamics at 3000K and cooling starting from 3000K are not
changed in my case?
Why does the script start from a folded structure instead of extended one?
Is that because there are some "high temperature" steps which can randomly
expand the structure, and therefore it doesn't matter the starting structue
is folded or expanded?
Since I only have PRE data, I commented out "NOE", "dihedral angle
restraints", "repulsive restraints for EDTA-DNA phosphate", "planerity
restraints", and "base-base positional database", and related parameters
(e.g.k_noe) as well.
The starting structure is 3 identical extended proteins atthe same position,
with segment id C1, C2, and C3. PDB, and PSF file are generated in a way
like:
############
evaluate ($ncount = 1)
while ($ncount < $copies) loop GENERATE
evaluate ($ncount = $ncount + 1)
evaluate ($chainname = "C" + encode($ncount))
duplicate
segid = $chainname
select = ( segid="C1")
end
end loop GENERATE
evaluate ($filename = $prefix+encode($copies)+".pdb")
evaluate ($structname = $prefix+encode($copies)+".psf")
#############
The "def setConstraints" part is changed as
#############
command("""
constraints
inter = (segid " ") (segid " ")
inter = (segid "C1") (segid "C1")
inter = (segid "C2") (segid "C2")
inter = (segid "C3") (segid "C3")
weights * 1 angl %f impr %f vdw %f end
end""" % ( k_ang, k_imp, scaleVdw) )
############
Now I am struggled, final lines in the log file is:
###############
test.py(502): return
test.py(861): print "cooling cycle - No.%d-" % i_cool
cooling cycle - No.0-
test.py(862): print "current bathTemp = %7.2f" % bathTemp
current bathTemp = 2405.00
test.py(863): dynamicsWithCheck(dyn, coolTimestep, bathTemp,
finalTime, maxCycle)
test.py(553): s.calcEnergy()
MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4)
and 0 GB exclusions
MAKINB: mode 3 found 3821 exclusions, 0 interactions(1-4) and
3821 GB exclusions
MAKINB: mode 3 found 3821 exclusions, 0 interactions(1-4) and
3821 GB exclusions
MAKINB: mode 3 found 3821 exclusions, 0 interactions(1-4) and
3821 GB exclusions
test.py(554): ok = 0
test.py(555): ni = 0
test.py(556): while ok == 0 :
test.py(557): pene = s.Epotential()
test.py(558): s.setNumSteps(maxcycles)
test.py(559): s.setStepsize( timestep )
test.py(560): s.setBathTemp( bath )
test.py(561): s.setFinalTime( finalTime )
test.py(562): s.setPrintInterval( 10 )
test.py(563): s.setETolerance( bath/1000 )
test.py(564): s.setResetCMInterval(10)
test.py(565): s.setResponseTime(20)
test.py(567): dyn.setMaxDeltaE(10000)
test.py(569): s.run()
*--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.002
--*
| E(kin)+E(poten)= 21110.576 E(kin)= 4449.966 temperature=
3238.358 |
| E(poten)= 16660.6104132 grad= nan ANGL=
30.9321704 |
| BOND= 12.0900990 CARB= 0.0000000 CDIH=
0.0000000 |
| COLL= 11088.9619476 COUP= 0.0000000 IMPR=
4833.2021617 |
| NOE= 0.0000000 ORIE= 0.0000000 PLAN=
0.0000000 |
| RAMA= 0.3039902 SANI= 0.0000000 VDW=
695.1200443 |
| XDIP= 0.0000000 g35c= 0.0000000 k33c=
0.0000000 |
| k48c= 0.0000000 k63c= 0.0000000 k6c=
0.0000000 |
| r74c= 0.0000000 s20c= 0.0000000 s57c=
0.0000000 |
*------------------------------------------------------------------------------*
InternalDynamics::step: caught assertion failure:
calcD_G: singular D matrix. Bad topology?
HEAP: maximum use= 18757102 current use= 17319788
############
Any hint to solve this? Thank you very much!!!!
Best wishes,
Jie-rong
2008/4/17, Charles at schwieters.org <Charles at schwieters.org>:
>
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>
> Hello Jie-rong--
>
>
> > To properly include solvent, you mean I should solvate the starting
> structure
> > and coordinate with water box or water sphere? What do you mean "an
> > appropriate" temperature?
> >
>
>
> room temperature, or whatever corresponds to your experiment. But let's
> forget about water for now, and concentrate on working with the given
> protocol.
>
>
> > I tried to run "saWithPreAll-3conf.py", however, came out some error
> > messages:
> >
> > The final few lines in the log file:
> > ###################################
> > %POWELL-ERR: Line search abandoned
>
>
> this is a normal message.
>
>
> >
> > The error from xterm window:
> > ############################
> > Traceback (most recent call last):
> > File "<string>", line 2, in ?
> > File "/Users/huang/XplorNIH/xplornih2.19/python/trace.py", line 180,
> in run
> > exec cmd in dict, dict
> > File "<string>", line 1, in ?
> > File "saWithPreAll-3conf.py", line 1091, in ?
> > structLoopAction=structLoopAction).run()
> > File "/Users/huang/XplorNIH/xplornih2.19/python/simulationTools.py",
> line
> > 229, in run
> > s.structLoopAction(s)
> > File "saWithPreAll-3conf.py", line 942, in structLoopAction
> > en[xn] = XplorPot(xn).calcEnergy().energy
> > AttributeError: 'float' object has no attribute 'energy'
>
>
> this is due to one of the few incompatible changes in Xplor-NIH in
> the past few years. Please change
> calcEnergy().energy
> to simply
> calcEnergy()
>
> My apologies for this change.
>
>
> > Besides, some questions about the script:
> > The input coordinate: random3Alts1.pdb is not an extended protein. Will
> it
> > be
> > exteneded later in the script (and where it is stated) or I can also
> start
> > from extended file?
>
>
> Do you want it extended? If so, place a
> import protocol
> protocol.genExtendedStructure()
> after reading the coordinates.
>
>
> >
> > What is "setTaucAtoms" and what is clock atoms? I don't really
> understand,
> > could you explain a little bit more?
>
>
> These pseudo atoms represent the value of tau_c (correlation time). The
> positions can be varied to optimize this value. Please see
> http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/prePot.html
>
>
> >
> > In "def setConstraints(k_ang, k_imp)" part, is there any relation
> between
> > "nconf" and the number of "ALT"s (e.g. ALT1, ALT2...)? In
> > "random3Alts1.pdb", there are only ALT1, ALT2, and ALT3, but in the
> script,
> > its up to 10 ALTs (0 to 9)? Any reason? or it doesn't matter?
>
>
> The script can deal with up to 10 chomophore conformations, but there
> are only three in random3Alts1.pdb.
>
>
> > What's the
> > difference between "inter = (segid "ALT1") (segid "ALT1")" and "inter =
> > (segid " ") (segid "ALT1")"?
> >
>
>
> These constraints interaction statements are the most difficult aspect
> of the script, and should be changed very carefully.
>
> inter = (segid "ALT1") (segid "ALT1")
>
> specifies interactions of ALT1 with itself.
> inter = (segid " ") (segid "ALT1")
> specifies interactions between ALT1 and the DNA. Note that the ALTs
> (different configurations of the TED chromophore) should not interact
> with each other, and, thus, there are no constraints interaction
> statements with cross terms (e.g. ALT1 with ALT2).
>
> I hope this helps--
>
> Charles
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