The adjacency list syntax changed in July 2014. The minimal requirement for most translations is to prefix the number of unpaired electrons with the letter u.
Example old syntax:
HXD13
1 C 0 {2,D}
2 C 0 {1,D} {3,S}
3 C 0 {2,S} {4,D}
4 C 0 {3,D} {5,S}
5 *1 C 0 {4,S} {6,S}
6 *2 C 0 {5,S}
Example new syntax:
HXD13
1 C u0 {2,D}
2 C u0 {1,D} {3,S}
3 C u0 {2,S} {4,D}
4 C u0 {3,D} {5,S}
5 *1 C u0 {4,S} {6,S}
6 *2 C u0 {5,S}
The new syntax, however, allows much greater flexibility, including definition of lone pairs, partial charges, wildcards, and molecule multiplicities, and was necessary to allow us to add Nitrogen chemistry. See :ref:`rmgpy.molecule.adjlist` for details of the new syntax.