Hi there, I tried to convert the ligand DDP from the format PDB to MOL2. This ligand can be found in the PDB 1IL5.
However, Open Babel was not able to detect the aromatic atoms correctly. For example, the nitrogen N1 was set as an amide (am) instead of aromatic (ar). I suspect that convert a PDB directly to Mol2 is not a good idea. I've realized that some ligands in a PDB format sometimes present some errors in the atoms classification. Does anyone know if a PDB conversion is not indicated? The file is in attachment, but it also can be found at http://www.rcsb.org/pdb/explore/explore.do?structureId=1IL5. 1IL5.pdb <http://forums.openbabel.org/file/n4659035/1IL5.pdb> -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Presto, an open source distributed SQL query engine for big data, initially developed by Facebook, enables you to easily query your data on Hadoop in a more interactive manner. Teradata is also now providing full enterprise support for Presto. Download a free open source copy now. http://pubads.g.doubleclick.net/gampad/clk?id=250295911&iu=/4140 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
