Hi Charles,
Thank you for your reply. I did modify the
'newrefine.py'(attached file) but got the following errors:
InternalDynamics::step:
large timestep detected. Halving.
%atoms "ALT2-35 -CYSP-SG2 " and
"ALT3-35 -CYSP-SG2 " only 0.01 A apart
InternalDynamics::step:
large timestep detected. Halving.
InternalDynamics::step: large
timestep detected. Halving.
InternalDynamics::step: large timestep
detected. Halving.
InternalDynamics::step: large timestep detected.
Halving.
InternalDynamics::step: large timestep detected. Halving.
InternalDynamics::step:
large timestep detected. Halving.
InternalDynamics::step: large
timestep detected. Halving.
InternalDynamics::step: large timestep
detected. Halving.
InternalDynamics::step: large timestep detected.
Halving.
InternalDynamics::step: large timestep detected. Halving.
InternalDynamics::step:
large timestep detected. Halving.
InternalDynamics::step: large
timestep detected. Halving.
InternalDynamics::step: stepsize too
small.
Traceback (most recent call last):
File "<string>",
line 2, in <module>
File
"/opt/xplor-nih-2.26/python/trace.py", line 180, in run
exec cmd
in dict, dict
File "<string>", line 1, in <module>
File "newRefine.py", line 634, in <module>
averagePotList=potList).run()
File
"/opt/xplor-nih-2.26/python/simulationTools.py", line 281, in run
s.structLoopAction(s)
File "newRefine.py", line 569, in
calcOneStructure
dyn.run()
File
"/opt/xplor-nih-2.26/python/ivm.py", line 465, in run
(done,s.stepsize_) = PublicIVM.step(s,s.stepsize());
File
"/opt/xplor-nih-2.26/python/wrappers/publicIVM.py", line 136, in step
def step(self, *args, **kwargs): return _publicIVM.PublicIVM_step(self,
*args, **kwargs)
_publicIVM.IVMError: IVM error: stepsize too small
PyInterp::command:
error executing: >execfile('newRefine.py')<
HEAP: maximum
use= 22720953 current use= 19890309
X-PLOR: total CPU time=
19.0100 s
X-PLOR: entry time at 19:24:50 7-Sep-10
X-PLOR: exit
time at 19:25:13 7-Sep-10
Also, I am not quite understand
the clock atom and tauc part. How are the initial values (resid 777-783;
taucapp=2.9,3.0) chosen?
I want to calculate form extended
structures, and the modified 'anneal.py'(attached file) did work. But in
the output file, there are VDW violations between conformers of the
same cysp like these:
viol% amount index restraint name
---------------------------------------------------------------------------
100.0
0.96 0 ( ALT1 7 CYSP SG1 ) ( ALT2 7 CYSP SG2 )
100.0
1.01 1 ( ALT1 7 CYSP SG1 ) ( ALT3 7 CYSP SG2 )
100.0
1.02 2 ( ALT1 7 CYSP SG2 ) ( ALT2 7 CYSP SG1 )
100.0
1.85 3 ( ALT1 7 CYSP SG2 ) ( ALT2 7 CYSP SG2 )
100.0
1.18 4 ( ALT1 7 CYSP SG2 ) ( ALT2 7 CYSP CL1 )
Are
these normal? I use MOLMOL to calculate the distance between 'OS1' and
'HN' atoms. The calculated ones are larger than the max distance in the
input '.tbl' files, but they were not reported in the '.viols' files.
Thank
you very much for your help!
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