[gmx-users] struggles with cyclic peptides

[Nikhil]

Hi Justin,
So your saying working with Gromacs for cyclic peptide is hopeless using 
available methods?
i tried all terminals
in  .tdb file  removing C ,O and H from -COOH so that only O will add up 
and before that removing O from the pdb ,i tired that but ends up with 
lots of errors.
i found in archives same issues as connection establishing with C-N but 
extra atoms at each terminals ..!

Anyway thanks for your replies