[gmx-users] [Beginner] How can I generate .gro and .top?

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 22 20:47:26 CET 2007

Hi Marcelo,

Are you actually interested in the characteristics of your
polyethyleneimine with four different substituents randomly arranged
on each unit? Or is it ok to have something which in a way resembles
sort of polyethyleneimine with four different substituents, which may
or may not give behaviour correspondent to real chemical substituents?
If the former is the case, you can't do with x2top, nor with PRODRG,
but you will need to do a proper parameterization. If the topology is
a black box to you, don't go there. If the latter is the case, you can
try to get separate topologies for your different building blocks and
use these to construct the whole chain. You may want to take a good
look at one of the ff*.rtp files together with the gromacs manual to
get a feel for the definitions of building blocks.

Hope it helps,


On 1/18/07, Marcelo de Freitas Lima <mflima at qmc.ufsc.br> wrote:
> ******
> > You may want to try x2top, but it will only work for simple molecules.
> >
> > --
> > David.
> ******
> > The answer is both yes and no. Gromacs can deal with non-proteins but
> > the force field may not be able to do it. In your case, what's the
> > monomer? Can you find some literature of it? Can you try pass the
> > monomer to the PRODRG?
> >
> > Yang Ye
> >
> > P.S.: From pdb to gro, you can use editconf.
> *******
> Thank you both David and Yang Ye,
> PRODRG can't handle that polymer (at least the one from the web site
> "The Dundee PRODRG2 Server") because the size is too far from the
> limit (~300 atoms). So I hadn't tried x2top yet for the same reason.
> The molecule is a derivative of polyethyleneimine with 4 different
> monomers distributed randomly.
> I will try to generate the ".gro" file by editconf, as you said,
> however the topology file continues a black box for me. If someone
> could help me...
> Thank you everybody,
> all the best,
> Marcelo
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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