[gmx-users] gromacs with carbohydrates

[Tsjerk Wassenaar]

The 45a3, 53a5 and 53a6 series of the GROMOS force fields contain
carbohydrate parameters. I would advise to use one these (especially because
of the treatment of the ring and connecting dihedrals).

Tsjerk

On 3/29/06, Hugo Verli <hverli at cbiot.ufrgs.br> wrote:
>
> Dear Andreas,
>
> As David mentioned, I think that prodrg is the best way to represent
> carbohydrates in GROMACS. I have simulated heparin and other carbohydrates
> (sulfated or not) both in solution and complexed with proteins, and had
> obtained a high level of accuracy with experimental data, as NMR, X-ray
> and
> mutagenesis. The results are fine both with GROMACS force field and with
> GROMOS96 force field.
>
> I only suggest a special attention to carbohydrate ring conformation. If
> it
> distort during the simulation I suggest that you fix it in the expected
> conformation by using improper dihedrals.
>
> Best regards,
>
> Hugo Verli.
>
> -----Mensagem original-----
> De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> Em
> nome de David van der Spoel
> Enviada em: quarta-feira, 29 de março de 2006 10:10
> Para: Discussion list for GROMACS users
> Assunto: Re: [gmx-users] gromacs with carbohydrates
>
> Andreas Steffen wrote:
> > hi,
> > is there an adequate forcefield in gromacs for dealing with
> > carbohydrates (cyclodextrin) or do I have to map the atoms to the
> > protein atom types?
> > Thanks in advance!
> > Andreas.
> >
> try starting with prodrg
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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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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