On 2012-10-17 15:15, David van der Spoel wrote: > Hi, > > I've done some G2 calculations on small molecules using Gaussian, and > each of these files contains 7 calculations. Babel crashes when trying > to read this: > > % curl http://folding.bmc.uu.se/222-trichloroethanol-g2.log > > 222-trichloroethanol-g2.log > > % babel -ig09 222-trichloroethanol-g2.log -osdf koko.sdf > Segmentation fault > > % babel -v > No output file or format spec! > Open Babel 2.3.1 -- Oct 4 2012 -- 19:42:21 > > Stack dump: > Program received signal EXC_BAD_ACCESS, Could not access memory. > Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000 > 0x00007fff8c1c54f0 in strlen () > (gdb) where > #0 0x00007fff8c1c54f0 in strlen () > #1 0x00007fff8bbda6d3 in std::string::operator+= () > #2 0x00000001015e0bdf in OpenBabel::GaussianOutputFormat::ReadMolecule () > #3 0x00000001000f9135 in OpenBabel::OBMoleculeFormat::ReadChemObjectImpl () > #4 0x00000001002738a4 in OpenBabel::OBMoleculeFormat::ReadChemObject () > #5 0x00000001000b4804 in OpenBabel::OBConversion::Convert () > #6 0x00000001000b4a91 in OpenBabel::OBConversion::Convert () > #7 0x00000001000b5020 in OpenBabel::OBConversion::FullConvert () > #8 0x0000000100002f44 in main () > > Is this a know problem?
The problem is due to a call to strchr at line 326 of gaussformat.cpp the result of which is not checked but assumed to be correct. comment += strchr(buffer,'=')+2; > > Is this kind of file supposed to be supported, including reading energy > terms etc.? > > Thanks, > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
