Dear gmx users,
I am trying to perform MD simulations of a DNA dodecamer complexed
with some ligands but I facing some problems to generate the ligands
topologies and insert Na ions to neutralize the system ! I have built
the first ligand.itp file by hand, what is very time consuming. So I
wonder if someone know a software or server (like PRODRG) able to
generate ligand topologies to the ffamber99 force field.
Also, I am wondering how to include the ions topology in the
GROMACS file ions.itp in order to make ffamber99 force field recognize
the ion topology.
With the best regards,
Tanos C. C. Franca.
Laboratory of Molecular Modeling Applyed to the Chemical and
Biological Defense (LMMCB)
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