Update FAQ

[mattwthompson]

I read through the FAQ and am tagging some sections as slightly or significantly out of date. I don't have the time to work on these now, so I'm noting them for future changes.

• "Can I use an AMBER (or GROMACS) topology/coordinate file as a starting point for applying a SMIRNOFF force field?"
  • This is no longer entirely impossible
• "What about starting from a PDB file?"
  • Missing discussion of recent capabilities of loading some PDB files
  • Possibly reading ligands from (some) PDB files would be enabled by Infer bond orders and formal charges #1828
• Add section on confusing UX of assigning partial charges fails if conformer generation fails #1741
• Add section on "Can I use an Amber force field with SMIRNOFF?"