Description
Is your feature request related to a problem? Please describe.
A common mode of user issues seems to be the use of defective PDB files that are noncompliant with the PDB standard by missing CONECT cards for HETATMs. This results in many hours of user confusion. The examples have several cases of this, e.g.:
https://github.com/openforcefield/openforcefield/blob/master/examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb
Describe the solution you'd like
We should at least add a warning to these examples, though there may be other programmatic changes we can make to help catch this common error.
Describe alternatives you've considered
If I could wave a magic wand and make the PDB format go away, I definitely would.
Genies were also considered, but no ancient cursèd oil lamps could be located.
Additional context
https://openforcefieldgroup.slack.com/archives/C9NGV68BY/p1599234563002200