[gmx-users] Using a rtp file for sugar
mattiofer at gmail.com
Wed Oct 5 16:48:23 CEST 2005
I just found pdb files of sugars in
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.
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?
> 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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