[gmx-users] large carbohydrates

[Tsjerk Wassenaar]

Hi Peter,

I know that the GROMOS building blocks also comprise the termini. You should
be able to add those to the terminal databases (.ntb and .ctb).
Shouldn't take too much time if you understand the format. Unfortunately I
have no time to spare now :(

Cheers,

Tsjerk

On 5/15/06, Peter I. Hansen <piha at kvl.dk> wrote:
>
> 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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-- 

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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