[gmx-users] Using a rtp file for sugar

Fernando Mattio mattiofer at gmail.com
Wed Oct 5 15:50:39 CEST 2005

 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?

GALB ffgmx.rtp - galactose-BC6H10O5- GLCA ffgmx.rtp - glucose-AC6H10O5- GLCB
ffgmx.rtp - glucose-BC6H10O5-

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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