[gmx-users] six member ring won't stay flat

[MD]

Hi Gromacs,

I have a modified side chain amino acid and it has a six member ring
attached to it. Regarding this ring I had dihedral angles taken care with
some 0s and some 180s. However, after minimization my structure looks very
strange, the ring is not flat and the dihedral angles in my settings didn't
seem to apply to the minimized structure at all. Any thoughts?

Thanks,

Ming