Known problems

See also issues.

• automatic update of links (see #25)
• Wrong NR5/NR6 atom types that should be NR15/NR16 (7k+ entries)
• chi* torsion names should be used for nonstandard amino acids including MSE
• torsion angle default sigma for sp2_sp2 may be too large (particularly chi5 of ARG)
• need information about deuterium containing monomers that were deleted #6 (monomer aliases?)
• peptide should define C-CA-N-H torsion, but some use different atoms instead of C (e.g. BP5), which will cause distorted H geometry (when linked)
• radical and H related issues, e.g. DKE/RFQ/NO/XX2 (not handled in #50)
• carboranes
• acedrg cannot handle 202 2FK