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

Marcelo de Freitas Lima mflima at qmc.ufsc.br
Thu Jan 18 23:52:59 CET 2007

> 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,


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