Hi, I'm not sure why pdb was the output format I was certainly not expecting it. On 19 Nov 2010, at 13:55, Pascal Muller wrote:
> Hi, > >> MASTER 0 0 0 0 0 0 0 0 16 0 16 0 >> END >> ENDMDL >> MODEL 3 >> COMPND UNNAMED >> AUTHOR GENERATED BY OPEN BABEL 2.3.0 > > I don't know if it will help, but the tag "END" should be the very > last line of the PDB file. There is only one occurence of "END" per > pdb file. > http://www.wwpdb.org/documentation/format23/sect11.html > > And ENDMDL is at the end of each model. > http://www.wwpdb.org/documentation/format23/sect9.html > > And I think that the COMPND and AUTHOR records are not allowed within > the MODEL record - but won't matter that much, I think :) > > Normally, it's the same molecule / same author for each model, only > the coordinates are modified. > > But could have e.g. (see > http://www.wwpdb.org/documentation/format23/sect2.html) > COMPND MOL_ID: 1; > COMPND 2 HEMOGLOBIN; > COMPND MOL_ID: 2; > COMPND 2 BENZENE > like in many PDB complex. > > Btw, compound name is lost when converting, with babel 2.2.3, .pdb to > .smi or .sdf. > > But I never use pdb format as multi-mol file, and I always convert my > protein-ligand pdb complex in mol2... :) > Never used obminimize too. > > Regards, > Pascal ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
