> obenergy -ff GAFF file.pdb > I get different bonds then when I run > obenergy -ff GAFF file.sdf > > Since the atomtyping is done based on smarts I wonder whether different > algorithms are used for generating smarts depending on the input file?
Different file types may or may not present full bonding information, esp. XYZ or PDB. Something like SDF is great because it provides bonds, valence, etc. (i.e., the full valence structure of the molecule). With PDB.. well, we have full bonding information for residues, but otherwise it depends on what's available in the CONECT records (if they exist). Normally, we have to at least do bond order perception. I'm pretty sure you asked over the summer - my group is working on some ML-based methods for improved bond order assignments and we'd be happy to collaborate. Obviously, once it's in good state, we'll put everything up, including the training and test sets (i.e., you can add problematic molecules to improve the training). Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
