Hi Leonardo,
the problem is that the COO- terminus entry in aminoacids.c.tdb uses atom “CB” as the third control atom for adding OT1 and OT2. Until it is fixed in the next release of the port, please edit the line "2 8 OT C CA CB " in aminoacids.c.tdb to "2 8 OT C CA N ". That should fix it.
Sorry for the inconvenience,
Andras