[gmx-users] amide plane

Abil Aliev abil4616 at yahoo.co.uk
Tue Dec 7 19:07:48 CET 2004

 i've checked a few runs with gromos 53a6 and can see
that the amide plane is not quite planar, but rather a
flat pyramid. if i measure a dihedral angle for GLY
CA-C-N-O, i get 166,5 dgr. what bothers me is that
having a pyramid means having a pyramid inversion (a
bit like N inversion in amines).

any comments?? incidentally the same angle with
namd/charmm is 178 dgr.

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