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

Yang Ye leafyoung81-group at yahoo.com
Thu Jan 18 16:16:32 CET 2007

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.

On 1/18/2007 9:37 PM, Marcelo de Freitas Lima wrote:
> Dear all,
> How can I generate a ".gro" and a ".top" from a ".pdb" file of a 
> synthetic polymer residue (548 atoms with a random distribution of 
> monomers)?
> There is some tutorial to use gromacs with strutures like that, 
> instead proteins?
> Problem:
> The PRODRG webserver can't convert my structure, because there is so 
> many atoms.
> Thank you all,
> All the best,
> Marcelo
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