Hi all, I can confirm that writing the pdbqt file works without problems on several Linux distributions (including some CentOS, RedHat and Debian Systems and derivates). Hence, unfortunately, I cannot try to find the location of the bug as I don't have a MacOS-system available.
It should not be too hard to add some simple debug output to the place where the output file is written to check where exactly the error happens. Although it's important to flush the output as shown below [1]. Maybe a programme like Valgrind could help to find the issue if it's memory related? You could also try to turn of optimization during the compilation. If it's a matter of trying to access memory that is already allocated by a different programme, the issue is more likely to occur with high optimization (at least that's what I experienced on Linux). It'd still need to be fixed though. Hope this helps, Torsten [1]: Example debug output (in case you don't know): std::cerr << "Debug: 1" << std::endl << std::flush; On Tue, 4 Aug 2015, David Hall wrote: > It seems I can reproduce the segfault on OS X Yosemite, but not on Ubuntu > 14.04. > > -David > > >> On Aug 4, 2015, at 8:02 PM, R. K. Belew <rbe...@ucsd.edu> wrote: >> >> update, if anyone is interested: it seems quite clear the >> bug is in the PDBQT output filter: >> >>>> obabel file1.pdbqt -O file2.pdbqt >>>> Segmentation fault: 11 >>>> obabel file1.pdbqt -O file2.pdb >>>> 1 molecule converted >> >> and has nothing particular to do with pybel; pybel is >> silently eating this fault and generating only partial >> output before it dies. >> >> Rik >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
