[gmx-users] amide plane

David spoel at xray.bmc.uu.se
Tue Dec 7 19:34:23 CET 2004

On Tue, 2004-12-07 at 18:07 +0000, Abil Aliev wrote:
>  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.
have you tried the OPLS force field or an older gromos?

have you checked the topology file?
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
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spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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