[gmx-users] amide plane

[Abil Aliev]

yes, oplsa seems better (~175 dgr). but i couldnt find
HYP entry in the rtp file for this. is there any way
to add this?

havent checked older gromos. didnt find anything wrong
with the topology file. what exactly needs checking?
here is a small fraction of the itp file:

    11          O      1    HYP      O      5     
-0.45    15.9994   ; qtot 1
    12          N      2    GLY      N      6     
-0.31    14.0067   ; qtot 0.69
    13          H      2    GLY      H      6      
0.31      1.008   ; qtot 1
    14        CH2      2    GLY     CA      7         
0     14.027   ; qtot 1
    15          C      2    GLY      C      8      
0.45     12.011   ; qtot 1.45
    16          O      2    GLY      O      8     
-0.45    15.9994   ; qtot 1
    17          N      3    PRO      N      9         
0    14.0067   ; qtot 1


 --- David <spoel at xray.bmc.uu.se> wrote: 
> 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.
>
________________________________________________________________________
> 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
> phone:  46 18 471 4205          fax: 46 18 511 755
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