[gmx-users] large carbohydrates

[Peter I. Hansen]

Hi

The 53a5 and 53a6 sets do have sugar residues, but it seems this is only 
designed for 1->4 linkages, and does not provides atoms for start and 
end groups. How do you propose to build a complete carbohydrate from this?

thanks, Peter

Tsjerk Wassenaar wrote:
> Hi Peter,
> 
> You can define a building block in the .rtp file. For the parameters you 
> should check out the GROMOS 43a5 force field (notably a paper by Roberto 
> Lins). Sugar parameters are also available in the 53a5 and 53a6 force 
> field sets, which I thought were on the contributions page.
> 
> Cheers,
> 
> Tsjerk
> 
> On 5/15/06, *Peter I. Hansen* <piha at kvl.dk <mailto:piha at kvl.dk>> wrote:
> 
>     Hello
> 
>     I'm trying to set up a larger carbohydrate for MD in gromacs. I've used
>     prodrg for smaller sugars, since pdb2gmx seems to fail due to lack of
>     residues in the forcefield. But, prodrg fails when the number of atoms
>     is larger than 300 (and for the beta version, 500 atoms).
>     Is there another way to do this setup? I only need poly-alpha-glucose,
>     so it's just one residue I miss.
> 
>     thanks, Peter
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> 
> 
> -- 
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
> 
> 
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