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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