There are many ways to do this. But if you are not expert, you can do the following

1) use make NA server (http://structure.usc.edu/make-na/server.html) to create a pdb.

2) use charmm-gui to generate input files for gromacs or amber (http://www.charmm-gui.org/?doc=input/pdbreader)

There are many ways to do this. But if you are not expert, you can do the following

1) use make NA server (http://structure.usc.edu/make-na/server.html) to create a pdb.

2) use charmm-gui to generate input files for gromacs or amber (http://www.charmm-gui.org/?doc=input/pdbreader)

Use NAB program of AmberTool which is very trustable for DNA. Then convert it to gromacs format by amber2gmx script. The script you can find in net. If you don't, then I'll give you. Follow articles of Arnab Mukherjee, IISER Pune, India, he has used this process and published many high impact papers. 

For generating input parameter files for molecular dynamics simulations in gromacs, you better use the ACPYPE tool. It is a handy tool, it can generate what ever you need. But the installation is a bit tricky. You should first install the latest AMBERTOOLS (http://ambermd.org/AmberTools16-get.html).  

For running a gromacs simulation and the step by step tutorial, i suggest this ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/). 

I hope they can be helpful for you

Best,

I have created a DNA pdb file using server (http://structure.usc.edu/make-na/server.html) to create a pdb.

When I try to load this pdb in xleap it shows missing new atom types

and could not able to save prmtop and inpcrd file for MD simulation