I am interested in carrying out some all atom molecular dynamics simulations of biomolecular systems that have different generations of PAMAM dendrimers.
Those .mdp files are not correct for running simulations with CHARMM; the nonbonded setup is wrong. More to the point, those aren't topologies :)
I don't know what "different generations" of the dendrimers means, but as far as their chemical structure, CHARMM should cover the chemical space needed to create the topologies, certainly under CGenFF. You can try the ParamChem web server, though I believe there are size limitations (i.e. it won't handle a huge polymer, but you can generate some sensible parameters for building blocks and create a topology from there).
Thank you Justin and Abel. I am aware of the tools and the literature that was pointed out. I was hoping to see if somebody actually has the charmm parameter and topology files.