Dimitri Maziuk wrote > On 11/17/2015 01:14 PM, Alexandre Fassio wrote: > >> 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". > > Like I said, I don't know of any software that will do what you want. In > 5A05.cif the first row of _struc_conn table is > > covale1 covale ? H GLC . C1 ? ? ? 1_555 H BGC . O4 ... > > which I believe means there's a covalent bond between GLC C1 and BGC O4. > > ICBW, > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
Maybe a software that does what I want doesn't exist yet. In fact, it could help. However, some PDBs structures have ligands covalently bonded. In these cases, the author preferred to deposit the structure with the ligand represented as fragments (other small ligands). For example, a cellobiose can be represented as two glucoses (GLCs). Thus, it is difficult to know without a previous knowledge, which ligand is represented by these two GLCs. In another case, I had a PDB with 8 ligands covalently bonded and I don't know which ligand in the CIF dictionary represents these 8 ligands. -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659047.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
