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.