[gmx-users] amide plane

[David]

On Tue, 2004-12-07 at 19:56 +0000, Abil Aliev wrote:
> 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?
> 
you have to copy the PRO entry and add the OH group in the ffoplsaa.rtp
file, and also check the ffoplsaa.hdb file.

> havent checked older gromos. didnt find anything wrong
> with the topology file. what exactly needs checking?
whether all dihedrals are made. If the particular angle is at HYP then
you should compare to other peptide bonds, because HYP may well be less
tested than other residues.


> 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
> > spoel at xray.bmc.uu.se    spoel at gromacs.org  
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> 		
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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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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