[gmx-developers] pdb2gmx segmentation fault

Michel Cuendet michel.cuendet at isb-sib.ch
Tue Jun 30 19:08:27 CEST 2009

Dear David,

Thanks for trying to reproduce this annoying SegFault. Yes, it works 
fine with the 4.0.x releases, and it seems that the problem appeared 
when the new residue numbering was introduced. I however need the 
development version of gmx, because I'm testing the CMAP implementation 
with charmm27.

I was really optimistic when I read your reply, so I immediately 
downloaded the GIT version of today, compiled on the machines at hand, 
and tested again with 2GUO_nowat.pdb.

Alas !

osx_gcc4.0.1 shared      : OK
i686_gcc4.2.4 shared     : SegFault     (chain A)
i686_gcc4.2.4 static     : SegFault     (chain A)
em64t_gcc3.4.6 static    : SegFault     (chain B)

This looks like a nasty, difficult to reproduce bug... It's annoying, 
because I would need to produce topologies on a Linux machine, not on my 

Thanks or your help,

> I am now doing this using the latest git source, but it works fine on my 
> Mac.
> However, with a slightly older develop code it fails. With the .4.0.x 
> release tit works fine though.
> It seems to be a temporary bug that was resolved again.
> Plz upgrade...

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