Hi,
I'm currently trying to calculate the structure of a covalently linked
homodimer using xplor v2.33 on Ubuntu 10.04 using only distance , talos
dihedrals, and h-bond restraints. At some point during the calculation,
there's an error that appears (shown below) about the step size being too
large then too small. I'm essentially using the same parameters as the
anneal.py found in the eginput>gb1_rdc example in the xplor package. I
have also used the same anneal.py file for the monomeric protein and
everything worked smoothly. The only difference between the monomeric and
dimeric protein is the number of restraints, which is doubled.
I also attached my logfile for more information if needed. Any help would
be really appreciated!
Thank you,
Marie-Laurence Tremblay, PhD candidate
Department of Biochemistry and Molecular Biology
Dalhousie University
Phone:902-494-4812
[stdin](1): execfile('round25.py')
[stdin](1): execfile('round25.py')
MAKINB: mode 3 found 15831 exclusions, 0 interactions(1-4) and
15831 GB exclusions
MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4)
and 0 GB exclusions
*--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t=
0.0015999 --*
| E(kin)+E(poten)= 20989.468 E(kin)= 6974.370 temperature=
3457.795 |
| E(poten)= 14015.0982135 grad= 67.5665364 ANGL=
2326.9185219 |
| BOND= 9.1756895 CDIH= 2906.9832523 HBDA=
8.1348803 |
| IMPR= 3231.5519843 RAMA= -0.5304373 VDW=
3770.5403615 |
| noe= 1762.3239610
|
*------------------------------------------------------------------------------*
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: 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: 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 "/Applications/xplor-nih-2.33/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "round25.py", line 364, in <module>
averagePotList=potList).run()
File "/Applications/xplor-nih-2.33/python/simulationTools.py", line 360,
in run
s.structLoopAction(s)
File "round25.py", line 324, in calcOneStructure
cool.run()
File "/Applications/xplor-nih-2.33/python/simulationTools.py", line 1481,
in run
s.runIVM(s.bathTemp)
File "/Applications/xplor-nih-2.33/python/simulationTools.py", line 1534,
in runIVM
s.ivm.run()
File "/Applications/xplor-nih-2.33/python/ivm.py", line 513, in run
(done,s.stepsize_) = PublicIVM.step(s,s.stepsize());
File "/Applications/xplor-nih-2.33/python/wrappers/publicIVM.py", line
137, 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('round25.py')<
HEAP: maximum use= 38465598 current use= 24334970
_______________________________________________
Xplor-nih mailing list
Xplor-nih@cake.cit.nih.gov
http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
