[gmx-users] Using a rtp file for sugar

[Tsjerk Wassenaar]

Hi Fernando,

You can indeed use genbox to add the sugar structures to your system. For
the topology I would discourage to use either the prodrg server or the gmx
force field parameters, unless the behaviour of the sugar is not really
important (but probably that's not why you put it in there). Carbohydrates
are often a bit problematic, but Roberto Lins has parameterized them for the
Gromos 45a3 force field. I don't know whether these have been contributed to
the Gromacs site already, otherwise I can try to dig up an .itp file of a
sugar with his parameters for you, which I should have lying around
somewhere. Mail me off-list with the sugars you need.

Cheers,

Tsjerk

On 10/5/05, David <spoel at xray.bmc.uu.se> wrote:
>
> On Wed, 2005-10-05 at 16:48 +0200, Fernando Mattio wrote:
> > Hi again,
> > I just found pdb files of sugars in
> > http://www.nyu.edu/pages/mathmol/library/sugars/
> > So I think the next step is to use the genbox, right? With this
> > should be possible to multiply my sugar molecules and to put them in
> > random positions. Well I am not sure about this because I am new as
> > Gromac user, so any consideration about would be helpful for me.
> You can use genconf for the sugars and then genbox for solvating them.
> You can generate a topology using prodrg.
>
>
> > Thanks again,
> > Fernando Mattio
> >
> > 2005/10/5, Fernando Mattio <mattiofer at gmail.com>:
> > Hi Tsjerk and Gromacs users,
> > Thank you for your answer Tsjerk, but I am still a little
> > bit confused. What I would like to have is a protein in a box
> > of water, with molecules of sugar present in the system, I
> > mean in random positions. So I think I don´t need sugar
> > chains...
> > What I understood from your answer is that I need an .itp
> > file of sugar to be added in the topology file, is it right?
> > The problem is that I could not find in the Gromacs files an
> > itp file for sugar, only .rtp, so do I have to create it or is
> > it already done somewhere that I could not find?
> >
> > Sugars
> >
> >
> > GALB
> > ffgmx.rtp
> > -
> > galactose-
> > B
> > C6H10O5
> > -
> > GLCA
> > ffgmx.rtp
> > -
> > glucose-A
> > C6H10O5
> > -
> > GLCB
> > ffgmx.rtp
> > -
> > glucose-B
> > C6H10O5
> > -
> >
> >
> > And then to "multiply" my molecules of sugar and to add
> > them to my system in random positions, what programs should I
> > use?
> >
> > Thank you very much in advance,
> > Fernando Mattio
> >
> >
> >
> > 2005/10/5, Tsjerk Wassenaar <tsjerkw at gmail.com>:
> > Hi Fernando,
> >
> > Unless you're trying to build sugar chains, you don't
> > need to make building blocks in the .rtp file. It is
> > better to use .itp files for them. Also, it's better
> > not to use the gmx force field, but rather the GROMOS
> > one, for which there should be good sugar parameters
> > available (by Roberto Lins).
> > And genbox doesn't use the .rtp file, it's only used
> > by pdb2gmx. Genbox will insert molecules from a
> > structure file (gro, pdb).
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> >
> > On 10/5/05, Fernando Mattio <mattiofer at gmail.com>
> > wrote:
> > Dear Gromacs users,
> >
> > I would like to insert some molecules of sugar
> > in a box with protein and water . So my idea
> > was to use the ffgmx.rtp file, but copying
> > only the information of for example GALB and
> > saving it as other .rtp file. It is the first
> > time that I am dealing with this kind of
> > topology file, and I would like to know if it
> > is the right way of using the Gromacs Building
> > Blocks.
> > Then with genbox I think it is possible to
> > create other sugar molecules from the .rtp
> > file and to add them to my system, is it
> > right?
> >
> > Thank you very much in advance!
> > Fernando Mattio
> >
> >
> >
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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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> --
> 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://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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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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