I think the easiest way is try to construct a gromacs topology file using pdb2gmx , using your PRODRG generated file as input and selecting one of the gromos forcefield options ( as the paper that you cite is based on this ff). If works, will mean that the topology generated with PRODRG is valid for run a simulation with gromos.

But without doing this, and only reading the abstract of this paper, I think that you are not going to be able, at elast not in a good way, but in the paper are proposing several points as “best practices” for parametrization of small molecules under the GROMOS force fields, try to take advantage of them.

If you want to use Amber force field in GROMACS for simulations, you can use acpype to generate Groamcs format topology. https://code.google.com/p/acpype/.

Youre asking about gromos, so an alternative to PRODGR is ATB . Take a look to this useful page

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

Also, you can construct the topology by hand, using pdb2gmx gromacs option

Mr. Melchor, this tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html) also says that pdb2gmx will work for an entry if it is already present in the .rtp file of the force field. But Piroxicam is not a part of any of the force fields provided with gromacs. So how can I use pdb2gmx ? According to Justin, pdb2gmx will give a fatal error while trying to pass the pdb structure file of an unrecognized entry (Piroxicam) through it (pdb2gmx).

you can make your topology with PRODRG then calculate your partial charges with quantum software like Gaussian 98 and modify your topology file with this new charges.