[gmx-users] large carbohydrates

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 15 14:14:46 CEST 2006

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.



On 5/15/06, Peter I. Hansen <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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