[gmx-developers] pdb2gmx segmentation fault

Ran Friedman r.friedman at bioc.uzh.ch
Tue Jul 7 13:05:52 CEST 2009


I have a similar problem (on linux, tried with few PDBs, this has only 1
pdb2gmx -f ~/Proteins/PM_II/PDB/3F9Q.pdb -o prot.gro

Processing chain 2 (213 atoms, 213 residues)
There are 213 donors and 213 acceptors
There are 67 hydrogen bonds
Segmentation fault

The problem is with the waters. It seems that the program crashes in
hizzi.c, in set_histp
(lines: 223-225)
  for(i=0; (i<natom); ) {
    if (strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name,"HIS") != 0)

Apparently *pdba->resinfo[pdba->atom[i].resind].name is not initialised
and this causes the problem to die. I couldn't get further so far.


Michel Cuendet wrote:
> 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 mac...
> Thanks or your help,
> Michel
>> 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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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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