[gmx-users] Using a rtp file for sugar

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 5 11:14:23 CEST 2005

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).



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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