Difficulties with the Molfile

  1. Z-cartesian coordinate may be zero for planar molecules (depending on how the molecule is oriented). If the Z coordinate is specified as 0.00000, some programs that process Molfiles may assume that this means this information is absent rather than zero, and act as if a 3D model does not actually exist!
  2. Another undesirable feature of the Molfile is that each atom is defined by a line break. Since line breaks are not the same on different Computer operating systems, transfer between such system can often "break" the Molfile.
  3. The Molfile defines exactly how atoms are connected to each other, and by which kind of bond. But this connection table may not be correct, or the bond types may not be adequate to map onto a molecular mechanics force field parameter. Thus it is quite often the case that a Molfile may not work correctly when subjected to mechanics modelling. Quantum mechanics modelling on the other hand will entirely ignore the connection table, and work out where the bonds are and of what type from first principles.