Hi,
I am trying to refine a model (obtained using fold.py) directly against proton
chemical shifts. I am not familiar with the older XPLOR syntax, but I followed
some of the suggestions in response to earlier questions about this.
I included the chemical shifts using the
command('''
@PROTSHIFTS:protons_setup.tbl
protons
potential harmonic
class alpha
force 10.0
error 0.3
@alpha.tbl
end
''')
potList.append(XplorPot('PROT'))
*Note: This is not the entire proton chemical shift list, just the list
containing the alpha chemical shifts (as atest).
This is the exact syntax in test/protoncshift2.inp
When I run the program, the proton chemical shifts do not seem to be
incorporated in the structure calculation and gives the error:
refine.py(406): dyn.run()
*--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.001 --*
| E(kin)+E(poten)= nan E(kin)= 949.429 temperature= 3092.391 |
| E(poten)= nan grad= nan ANGL= 12.3546108 |
| BOND= 0.2960960 IMPR= 0.2828998 PROT= nan |
| Vgyr= 0.0161210 hb= -26.9585982 noe= 20.9643480 |
| repel= 3.0036906 repel14= 0.0000000 torsionDB= 2.1315950 |
*------------------------------------------------------------------------------*
eigen: 2 off-diagonal elements on an intermediate tridiagonal form did not
converge to zero.
Traceback (most recent call last):
File "/opt/xplor-nih-3.2/python/simulationTools.py", line 602, in run
s.structLoopAction(s)
File "refine.py", line 406, in calcOneStructure
dyn.run()
File "/opt/xplor-nih-3.2/python/ivm.py", line 569, in run
(done,s.stepsize_) = PublicIVM.step(s,s.stepsize());
File "/opt/xplor-nih-3.2/python/wrappers/publicIVM.py", line 202, in step
return _publicIVM.PublicIVM_step(self, *args, **kwargs)
SystemError: xplor-nih error: eigen: 2 off-diagonal elements on an intermediate
tridiagonal form did not converge to zero.
Error calculating structure 0: xplor-nih error: eigen: 2 off-diagonal elements
on an intermediate tridiagonal form did not converge to zero.
eigen: 2 off-diagonal elements on an intermediate tridiagonal form did not
converge to zero.
Traceback (most recent call last):
File "/opt/xplor-nih-3.2/python/simulationTools.py", line 602, in run
s.structLoopAction(s)
File "refine.py", line 406, in calcOneStructure
dyn.run()
File "/opt/xplor-nih-3.2/python/ivm.py", line 569, in run
(done,s.stepsize_) = PublicIVM.step(s,s.stepsize());
File "/opt/xplor-nih-3.2/python/wrappers/publicIVM.py", line 202, in step
return _publicIVM.PublicIVM_step(self, *args, **kwargs)
SystemError: xplor-nih error: eigen: 2 off-diagonal elements on an intermediate
tridiagonal form did not converge to zero.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/opt/xplor-nih-3.2/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/opt/xplor-nih-3.2/python/xplorInit.py", line 122, in execfile
exec(code, globals, locals)
File "refine.py", line 459, in <module>
averageCompSel="not resname ANI and not name H*" ).run()
File "/opt/xplor-nih-3.2/python/simulationTools.py", line 612, in run
nameSuffix=".crash")
File "/opt/xplor-nih-3.2/python/simulationTools.py", line 1248, in
writeStructure
makeBackup)
File "/opt/xplor-nih-3.2/python/simulationTools.py", line 1313, in
writeStructure
analyzeFilename)
File "/opt/xplor-nih-3.2/python/termAnalysis.py", line 242, in analyze
totEnergy = potList.calcEnergy()
File "/opt/xplor-nih-3.2/python/potProxy.py", line 88, in method
return getattr(object.__getattribute__(self, "_obj"), name)(*args, **kw)
File "/opt/xplor-nih-3.2/python/wrappers/potList.py", line 119, in calcEnergy
return _potList.rc_Pot_calcEnergy(self, *args, **kwargs)
SystemError: xplor-nih error: eigen: 2 off-diagonal elements on an intermediate
tridiagonal form did not converge to zero.
PyInterp::command: error executing: >xplor.execfile('refine.py')<
Please suggest how to fix this error.
Thanks a lot,
Ishita
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