[MMTK] Segmentation fault, normal modes calculation

hinsen at cnrs-orleans.fr hinsen at cnrs-orleans.fr
Fri Jan 5 21:50:10 CET 2007


On 05.01.2007, at 11:23, Lars Skjærven wrote:

> I am trying to calculate the normal modes of a large chaperon (GroEL/
> GroES complex, pdb code: 2cgt/1aon/1xck/2eu1). We know that these pdb-
> files have some missing residues, which we think may cause the
> problem.

That is certainly not the cause. Whatever might be wrong with the  
input files can at worst cause Python error messages.

> I have tried different methods, but they all return the same
> error. Namely "Segmentation fault". No other details are written to
> the screen. Running throught the gdb we found that it crashes at line
> 668 in MMTK_forcefield.c. This happens both om x86 and AMD 64 system.

A segmentation fault means that something goes wrong in the C code,  
either MMTK's C modules or the CLAPACK routines that are used in  
normal mode calculations.

Could you tell me which versions of Python and MMTK you are using?

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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