Periodic structure to Tinker MM3 - segmentation fault

[SanderBorgmans]

• [x] I believe this to be a bug with Open Babel
• [ ] This is a feature request

Environment Information

Open Babel version: 2.4.1 (or the 2.3.2 GUI version) Operating system and version: CentOS Linux 7 (Core)

Expected Behavior

Converting a periodic structure (e.g. .pdb file) to Tinker MM3 format.

Actual Behavior

Because of the periodic boundary conditions, it appears the bonds can not be recognized and the MM3 atom types can not be derived, leading to a segmentation fault. However the MM2 atom types can be derived (dropping the -x3 option). I don't mind the bonds not being recognized, I could just create a 3x3x3 supercell and look at the atom types of the central cell.

Steps to Reproduce

obabel -ixyz test.xyz -otxyz -x3 test.zip

[welcome[bot]]

Thanks for opening your first issue here! Be sure to follow the issue template!

[fredrikw]

The first thing to try is with a recent version of Open Babel if you have the possibility. 2.4.1 is rather old.

[SanderBorgmans]

@fredrikw Thanks for your response. The same issue arises with the newest version of openbabel (3.1.1)