#861 turbomole-generated g98 file crashes openbabel

2.3.x
open
nobody
None
1
2013-05-18
2013-02-02
No

Loading the attached file generated with aoforce2g98
http://www.turbomole-gmbh.com/manuals/version_6_4/Documentation_html/node9.html
produces good results with obabel 2.3.0 under OS X (molecule is benzonitrile):

% obabel -V
Open Babel 2.3.0 -- Oct 26 2010 -- 13:39:03
% obabel -o smi tmp/benzonitrile.g98
c1(ccccc1)C#N tmp/benzonitrile.g98
1 molecule converted

but crashes openbabel with 2.3.1 on Windows XP, and segfaults Linux (up-to-date Debian Wheezy—openbabel-2.3.1-dfsg-4).

This may be related to bug #860.

1 Attachments

Discussion

  • Mathias Laurin

    Mathias Laurin - 2013-02-03

    I have compiled openbabel-2.3.0 from source on my linux box (Debian wheezy) following the instructions on you website and can confirm that the molecular coordinates from my g98 file are parsed correctly with 2.3.0. That is, I have compiled openbabel on the exact same computer with the exact same config that was crashing with openbabel 2.3.1. It clearly appears that I uncovered a regression.

    By the way, you library does exactly what I need with a nice API so that I am very interested in seeing it fixed!

     
  • Chris Morley

    Chris Morley - 2013-02-17

    With the trunk code at r5063 VC10 build on Windows 7, benzonitrile.g98 is read ok for me, at least as far as the structure and 33 vibrational frequencies.

     
  • Mathias Laurin

    Mathias Laurin - 2013-05-13

    I have compiled the latest SVN yesterday in Debian stable:
    % obabel -V
    Open Babel 2.3.2 -- May 12 2013 -- 21:32:51

    The file does not crash Open Babel, but it is not converted either:
    % obabel -o smi tmp/benzonitrile.g98
    0 molecules converted

    I am also compiling on Windows and will see what I get.

     
  • Mathias Laurin

    Mathias Laurin - 2013-05-18

    I could convert all the files I tried on Windows but I still have no success on Linux, after compiling from SVN in both cases. Molden also converts well on Windows but not on my Debian.

    On Linux I have now tried to compile once with eigen2 and once with eigen3 but it made no difference.

     
    Last edit: Mathias Laurin 2013-05-18

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks