[gmx-users] Sugars as building blocks

[Daan van Aalten]

Hi Lieven

Have you tried the PRODRG server at
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html
This will make any carbohydrate structure you like within certain size
limitations.

cheers

Daan

On Mon, 7 Jan 2002, Lieven Buts wrote:

> 
>   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
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD 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 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O