[gmx-users] cyclic peptide dynamics. peptidic bond

[Giacomo Bastianelli]

I have a cyclic peptide and I would like to run a MD. unfortunately each 
time I run
pdbgmx2, it changes the peptidic bond at the cyclization residues to a 
"messy" bond.
I tried to fix it manually but it makes gromacs breaking the peptidic 
bond releasing
the linear peptide during the dynamics.

Thanks in advance!

Giacomo