[gmx-users] large carbohydrates

[Tsjerk Wassenaar]

Oops, that should read just .tdb for terminal database...

Sorry,

Tsjerk

On 5/15/06, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> 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
>



-- 

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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