[gmx-users] sugar improper dihedrals - ijkl or ikjl ?!

[Daan van Aalten]

Peter

For the definition of an improper dihedral atom IJKL:

I is the central atom (so the bonds I-J, I-K, I-L exist)

changing the order of any pair selected from JKL changes the sign of the
improper.

So changing from alpha to beta linked glucose is either flipping the
sign of the improper dihedral value (either +35.6 or -35.6) OR changing
IJKL to IJLK (for instance).

Daan

On Fri, 27 Jun 2003, Peter Bond wrote:

>
> Hi all,
>
> I'm trying to perform simulations of sugar units joined
> by a 1,4 linkage. I'd like to try both alpha and beta configurations of the
> linkage (i.e. the connecting exocyclic ester oxygen below or above the sugar ring
> planes). However, I'm not sure how to change between alpha or beta.
>
> As far as I can see, looking at the GROMOS96  parameters for alpha-glucose,
> beta-glucose, and beta-galactose, the only difference around the oxygen in
> question is the improper dihedral for the following atoms in the sugar ring:
>
>   ------O5
>   |     |
>   --C2-C1-C0-  (C0 being the ester oxygen connecting the two sugar units)
>
> For the alpha form, the improper dihedral is C1-O5-C0-C2
> For the beta form, the improper dihedral is C1-C0-O5-C2
>
> So my question is... is the result of an improper dihedral dependent on the
> order of atoms j and k (as defined in the manual)? Or are the alpha and beta
> configurations produced by something I haven't noticed?
>
> Many thanks for any responses,
> Pete Bond.
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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