On 12/03/2012 23:18, baratron wrote: > Hi all, > > I'm trying to find the quickest way to get ligands from the PDB website into > .mol2 format for use in another program. > 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 > 2 XX 4.6490 11.0350 23.3060 Du 1 LIG1 0.0000 > 3 XX 4.0200 9.8040 23.4780 Du 1 LIG1 0.0000 > etc. > > I searched on Google and the Nabble site& couldn't find anyone else having > problems converting from .sdf to .mol2. I'm assuming there's something > "special" or "different" about the ligand .sdf files from the PDB website, > but I don't know what that is. The entries in the SDF file like A 14 C5' are being interpreted as an alternative representation (alias) rather than additional information (atom types?), which OpenBabel does not understand. It sets the original atom to 0 atomic number, which is perhaps unnecessary. The is now altered in the development code, so that the basic structure is converted properly, although the warnings are still there. Is there a need for an option to capture the additional information? Chris ------------------------------------------------------------------------------ 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
