5. I read MOL2 files from HyperChem into Spartan or Sybyl and get wrong types.

When HyperChem writes MOL2 files, it writes the element correctly, but uses the default atom type (Du) for all atoms. This was a deliberate design compromise, to avoid having to map all of the four HyperChem forcefield type sets (each with completely user definable types!) to the set of types in the current Tripos force field (which could change, though we don't know if a Tripos user can change their definitions or not). At one point we considered making the MOL2 filter read-only because of this, but opted for writing with default types instead. Too bad neither Tripos or Wavefunction offer the ability to assign types based on user-editable rules like HyperChem can. ;-)

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