Hi all,
I am new to xplor nih.
I am running calculations on a modular protein (4 modules) of 270 amino
acids. I am trying to refine the NMR structure calculated by someoneelse
(with cyana followed with minimization with cns) using the same restraints
+ 2 sets of dipolar couplings (NH only) in 2 different media (phage and
peg). I am using the refine.py script. So the tensors are allowed to vary,
but I have an initial guess from Module on the preliminary NMR structures.
The sole changes I have made in the refine.py script concern the restraint
files.
The tensors were introduced with 700 and 701 numbering (as the residue
numbers for my protein begin at 355 and finish at 626.
The modules are supposed to have only a limited conformational freedom,
and I have maintained the gyration potential (does -it make sense for an
elongated modular protein which is highly anisotropic? (estimated
anisotropy of 4)?
The calculation fails to finish,
with this error.
refinement1234.py(337): protocol.initDynamics(dyn,
refinement1234.py(338): potList=potList, #
potential terms to use
refinement1234.py(339): bathTemp=init_t,
refinement1234.py(340): initVelocities=1,
refinement1234.py(343): printInterval=100)
refinement1234.py(345): dyn.setETolerance( init_t/100 ) #used to det.
stepsize. default: t/1000
refinement1234.py(346): dyn.run()
MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and
0 GB exclusions
MAKINB: mode 3 found 12172 exclusions, 0 interactions(1-4) and
12172 GB exclusions
*--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t=
0.001 --*
| E(kin)+E(poten)= nan E(kin)= 4341.138 temperature=
2889.629 |
| E(poten)= nan grad= nan ANGL=
66.7351079 |
| BOND= 1.7099773 CDIH= 99.7048545 HBDA=
nan |
| IMPR= 1.8225389 RAMA= -2.6377402 VDW=
19.7891008 |
| Vgyr= 12721.0179159 noe= 33.4141355 rdc=
129.1452028 |
*------------------------------------------------------------------------------*
eigen: 2 off-diagonal elements on an intermediate tridiagonal form did not
converge to zero.
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/trace.py", line
180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "refinement1234.py", line 398, in <module>
averageCompSel="not resname ANI and not name H*" ).run()
File
"/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/simulationTools.py",
line 281, in run
s.structLoopAction(s)
File "refinement1234.py", line 346, in calcOneStructure
dyn.run()
File "/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/ivm.py", line
465, in run
(done,s.stepsize_) = PublicIVM.step(s,s.stepsize());
File
"/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/wrappers/publicIVM.py",
line 136, in step
def step(self, *args, **kwargs): 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.
PyInterp::command: error executing: >execfile('refinement1234.py')<
HEAP: maximum use= 28019993 current use= 20384832
Any help would be greatly appreciated!
--
H?l?ne D?m?n?, PhD
Centre de Biochimie Structurale
UMR 5548 CNRS-UM1-INSERM UMR 554
29, rue de Navacelles
34090 Montpellier Cedex
France
Tel: +33 (0) 4 67 41 77 01
Fax: +33 (0) 4 67 41 79 13
e-mail: Helene.Demene at cbs.cnrs.fr
--
Passerelle antivirus CBS
