Hello Till-- > > I still have bad news however: I tried using the current version of > Xplor-NIH (3.2) on two different machines (one running Fedora 31 on > Linux-Kernel 5.8.18, the other openSUSE 15.1, Linux-Kernel > 4.12.14). In both cases I get a termination with the same error as > before updating. I would really like to troubleshoot this, but as of > now I cannot figure out what is happening or how to reproduce > failure/success in these cases. I will update you as soon as I find > the time to dig deeper into the IVM setup, and of course, all hints > are highly appreciated. >
Please clarify that this is using the run.py script you sent me
(attached below), and that the error message you get is
calcD_G: singular D matrix: { { 0 } }
H matrix: { { 0.749263, 0.556428, 0.359155, 0, 0, 0 } }
node level: 2
number of children: 1
atoms:
2545 ANI 5000 Z : { 0.727034, 0.536782, 0.339489 }
InternalDynamics::step: caught assertion failure:
calcD_G: singular D matrix. Bad topology?
Traceback (most recent call last):
File "/opt/xplor-nih-3.0.3/python/simulationTools.py", line 574, in run
s.structLoopAction(s)
File "./run.py", line 380, in anneal
torsionDynamics.run()
File "/opt/xplor-nih-3.0.3/python/ivm.py", line 569, in run
(done,s.stepsize_) = PublicIVM.step(s,s.stepsize());
File "/opt/xplor-nih-3.0.3/python/wrappers/publicIVM.py", line 202, in
step
return _publicIVM.PublicIVM_step(self, *args, **kwargs)
_publicIVM.IVMError: IVM error: calcD_G: singular D matrix. Bad topology?
Error calculating structure 1: IVM error: calcD_G: singular D matrix. Bad
topology?
This message probably indicates a topology misconfiguration for the
pseudo-atoms used to describe the alignment tensor. With the attached
file I get no such error. Is there some difference?
Charles
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run.py
Description: Binary data
