Hi Billy,

  1.  Firstly, why is that gromacs reads MYR as residue 2 and not 1? What does 
it say in your PDB file?
  2.  There is no atom labelled C in your MYR atom list. Looks like you have 
listed atom C in the dihedral type (ffnonbonded.itp), change that.
  3.  If you think it is not recognizing the link between MYR and B3K, then in 
the aminoacids.rtp file, for B3K, check if in the improper dihedral (involving 
terminal N) if there is atom C listed instead of C1. If yes, change it to C1.

Hope this helps,
Neena
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