[gmx-users] Sugars as building blocks

[Lieven Buts]

  Hello everyone,

  I would like to use GROMACS 3.0 for modelling
interactions between carbohydrates and proteins.
The ligands are oligosaccharides consisting
of mannose, glucose and N-acetylglucosamine
monomers, linked by different glycosidic linkages.
For instance, I would like to look at the
mannose(alpha1,x)mannose isomers (x=2,3,4,6).

  I have looked at the existing topology definitions
and found building blocks for alpha end beta glucose 
(GLCA and GLCB) and I am now thinking about the best 
way to define the topologies. Does anyone have any 
suggestions?



-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel