[gmx-users] Linking MYR residue to N-terminus using pdb2gmx

[Neena Susan Eappen]

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