Thanks a lot for your suggestions! I still have some (or lots of) questions
:)
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?
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
POWELL: Current coordinates set to last minimum
X-PLOR>
X-PLOR>end
saWithPreAll-3conf.py(933): dyn.resetReuse()
saWithPreAll-3conf.py(934): dyn.init()
saWithPreAll-3conf.py(935): dyn.calcEnergy()
saWithPreAll-3conf.py(937): outFile =
PDBTool("../Structures/3confWithPreAll%d.pdb" % (loopInfo.count+1))
saWithPreAll-3conf.py(939): en = {}
saWithPreAll-3conf.py(940): eAll = dyn.Epotential()
saWithPreAll-3conf.py(941): for xn in xpTerms :
saWithPreAll-3conf.py(942): en[xn] = XplorPot(xn).calcEnergy().energy
HEAP: maximum use= 17853510 current use= 13229777
X-PLOR: total CPU time= 276.4829 s
X-PLOR: entry time at 11:13:46 17-Apr-08
X-PLOR: exit time at 11:18:25 17-Apr-08
###################################
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'
PyInterp::command: error executing: >execfile('saWithPreAll-3conf.py')<
###########################
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?
What is "setTaucAtoms" and what is clock atoms? I don't really understand,
could you explain a little bit more?
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? What's the
difference between "inter = (segid "ALT1") (segid "ALT1")" and "inter =
(segid " ") (segid "ALT1")"?
Thanks for reading through these questions,
Best wishes,
Jie-rong
2008/4/15, Charles at schwieters.org <Charles at schwieters.org>:
>
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> Hash: SHA1
>
>
> Hello Jie-rong--
>
>
> > Instead of getting a refined structure, I am trying to have some sets or
> > contacts of conformation in a denatured protein with PRE
> restraints. One of
> > the currently used methods is applied in Michele Vendruscolo's group
> (e.g.
> > Dedmon et al, 2005 JACS, 127, 476-477). They calculated up to 20 copies
> of
> > extended protein together with long distance restraints by means of
> CHARMM
> > program.
>
>
> This sort of method depends critically on modelling, so you need to be
> careful to use a realistic force field properly including solvent effects.
>
>
> > One similar way in Xplor should be "ensemble.inp", I think.
>
>
> That script is not appropriate for extended structures with few
> restraints: there are no solvent effects included and electrostatics are
> disabled.
>
>
> > However, there is no "ensemble" parameter in PMAG (as in ensemble.inp
> "NOE
> > ensemble on end end") if I want to use delta R2 directly. If I want to
> > convert PRE into distance, it is also troubled me, because I am not sure
> > whether one can use the same energy function correctly.
>
>
> To refine directly against PRE, please use the Python module prePot, as
> in
> http://spin.niddk.nih.gov/clore/Software/pre_distribute.tar.Z
>
>
> > For example,
> > equation (18.6) in the Manual (potential = biharmonic) and equation (13)
> in
> > Iwahara 2004 JACS, is that possible convert the standard error of delta
> r2
> > into upper bound and lower bond limits?
>
>
> That work did not convert PRE data to distance bounds.
>
>
> >
> > Besides, the script from Iwahara 2004 JACS is simulated annealing with
> > multiple ligand to average the conformation ensemble, right? I am
> wondering
> > where the ensemble calculation is called in this script, and in which
> kind of
> > restraint, in dintance or in relaxation rate? (as equations (13) (15) in
> > Iwahara 2004 JACS)
>
>
> That work directly refines against PRE data, as in the script cited
> above. In these scripts, the ensemble was built manually in the PSF.
>
> Since you're trying to simulate a partially-structured protein, you
> will have to modify the scripts appropriately to properly include
> solvent at an appropriate temperature.
>
> hope this helps--
> Charles
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