Dimitri Maziuk wrote > On 11/17/2015 10:34 AM, Alexandre Fassio 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. If you have any suggestion, >> it'll be welcome. > > If you mean in a macromolecule PDB structure, you can download the mmCIF > file and take a look at _struct_conn table. I don't know of any software > that would help much: both we and RCSB have a number of parser packages, > but they'll just get you the table. You'll have to figure it out from > there. > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > ------------------------------------------------------------------------------ > > _______________________________________________ > OpenBabel-discuss mailing list
> OpenBabel-discuss@.sourceforge > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > signature.asc (197 bytes) > <http://forums.openbabel.org/attachment/4659041/0/signature.asc> Dimitri Maziuk, I've tried to use the mmCIF but I wasn't able to convert a ligand in the mmCIF format to MOL2 by using Open Babel. For some reason that I don't know, I always got the message "0 molecules converted". -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659043.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
