See link for all-atom PDB of urea

http://atb.uq.edu.au/molecule.py?molid=102073#panel-md

First of all this database is new for me. Thanks for introducing me this one. I tried to use pdb2gmx by downloading pdb file. But then it shows like this:

Residue 'QKMZ' not found in residue topology database

I'd probably skip the pdb2gmx step. If I were in your situation, I'd look online for *.itp files for urea. Ideally, you'll find an *.itp file for urea that already exists for your forcefield of choice. For instance, I typically use the CHARMM-36m forcefield for simulations, and am fairly certain there are parameters for urea solvents, so I'd specifically look for an *.itp file for urea for the CHARMM-36m forcefield. Anyway, the point is, once you have an *.itp from your desired forcefield, you can adjust the naming scheme in the pdb file (from the link I shared) to reflect the naming scheme in the *.itp. Eventually, you'll also have to add that *.itp to your topol.top file.

Does that make sense?

This sounds good. I got .itp file and with that its works. Thank you JD Tamucci for your time.