Geoff Hutchison wrote >> Indeed, we've tried the SDF and it is a good option. However, some small >> ligands have covalent bonds with other small ligands and by using the SDF >> format we won't able to detect it correctly. > > Can you give us some concrete examples of what you mean? > > -Geoff > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list
> OpenBabel-discuss@.sourceforge > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss Sure Geoff. My first example is the Cellobiose (id CBI) that is a disaccharide. Sometimes, this ligand is found represented as two glucoses (GLC). If you want, you can see an example in the PDB 5A05 (http://www.rcsb.org/pdb/explore/explore.do?structureId=5A05). Another example is in attachment. This file was extracted from the PDB 1H4P and it has 8 ligands. lig_example.pdb <http://forums.openbabel.org/file/n4659042/lig_example.pdb> If you open these examples in Pymol, for example, you'll see the ligands covalently bonded. In my work, I need to analyze the pharmacophore properties of the atoms. If I use the SDF of only one ligand I'll not consider the covalent bonds, thus this will not generate a properly analysis. Thanks -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659042.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
