[MMTK] Segmentation fault, normal modes calculation

Lars Skjærven larsss at gmail.com
Mon Jan 8 10:31:08 CET 2007


Hi,

The newest versions we tested on was Python 2.4.3 and MMTK 2.5.7.

Lars

On Jan 5, 2007, at 9:50 PM, hinsen at cnrs-orleans.fr wrote:

> 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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