Alexandre Fassio wrote > > 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 Sorry, I made a mistake. The PDB 5A05 does not have a Cellobiose (CBI) represented by two glucoses. Even so, this PDB has some examples of ligands covalently bonded. -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659044.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
