Hi, > I thought it would be quicker to download the ligands separately and convert > them from .sdf format to .mol2 format, but something weird happens when I do > that. If I run the OpenBabel program from command line, I get lots of > warning messages: > ============================== > *** Open Babel Warning in Expand > Alias CL1 was not chemically interpreted
> And then the output .mol2 file is missing all of the information about > chemical elements. They are all replaced with dummy atoms: > 1 XX 6.3250 11.0900 22.6650 Du 1 LIG1 0.0000 > Any ideas? In the sdf, delete the lines after the connection table until "M END". A 1 C12 A 2 C13 ... I don't know the goal of these lines. Or, with the HET id, get the smiles, e.g. wget http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=DX9 grep -A7 "Isomeric SMILES" ligandsummary.do\?hetId\=DX9 | grep stringWrapper Could probably get the smiles from PubChem too. Regards, Pascal ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
