[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 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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