[gmx-users] a question for generating a *.top file using pdb2gmx

[Zhen Qin]

Dear gromacs users,
  I have a question for using pdb2gmx to generate a *.top file for a
special protein. The protein looks like this:
NH-(CO-amino acid-NH)n-CO-cyclopropane-CO-(NH-amino acid-CO)m-NH
  The middle part is not a regular amino acids. I add the information
of -CO-cyclopropane-CO- to ffoplsaa.rtp as a residue, which has two C
terminal, and no N terminal.
  However, when I used  "pdb2gmx -f protein.pdb -p protein.top -inter"
to generate the protein.top file, the bond connections between the
middle part and its neighbour residues were not established, neither
were the corresponding bond angles or dihedrals. Do you have any
suggestions for making a topology file for such kind of protein?

 Thank you very much!

-Zhen

Have a good day !  ^&^