I work with molecular crystals and was very interested in the UFF implementation in OpenBabel. Unfortunately, it seems that periodic boundaries are not used for any of the atom typing, bond calculation or force field calculations. I noticed that periodic boundaries are one of the version 3 goals; is this something that is underway? Looking at the code this seems far from trivial to implement.
As an alternative, I decided to just use the powerful atom and bond typing systems from my Python code to setup UFF calculations elsewhere, but have encountered another problem. I can extract the types and bonds using pybel after feeding the OBMol to a Setup() of OBForceField etc. however, in order to ensure that the atoms at the edge of the cell are typed correctly, I generate a 3x3x3 supercell with the idea to take the atoms from the centre. This generates about 8000 atoms in my test system and during the setup of the forcefield the memory shoots up and crashes the python process (usually without any explicit error). After some digging and using obenergy etc., I see that the atom typing works as they are printed and the vdW setup step is using all the memory and causing the crashing. As far as I can tell there is no way to decouple the individual parts of the setup using the python bindings: .SetTypes() only works if ._mol has been set, but _mol is only set through .Setup() from the bindings. I could probably hack together a c++ tool or modify my compile to get the required result but would prefer a simple way to achieve this with the python bindings alone. Is there something I'm missing, or a better way to get the UFF atom types? Many thanks, Tom ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
