You can download structure, topology and parameter files for 230 different non-natural amino acids from  the SwissSidechain site  http://www.swisssidechain.ch/index.php, as well as plug-ins for PyMOL and UCSF Chimera that allow you to use these programs to mutate residues in a structure to one of these side chains. 

SwissSidechain: a molecular and structural database of non-natural sidechains

Gfeller D, Michielin O, Zoete V; Nucleic Acids Research, 41, D327-D332 (2013)

http://www.swisssidechain.ch/data/Gfeller_2013_1.pdf

You can download structure, topology and parameter files for 230 different non-natural amino acids from  the SwissSidechain site  http://www.swisssidechain.ch/index.php, as well as plug-ins for PyMOL and UCSF Chimera that allow you to use these programs to mutate residues in a structure to one of these side chains. 

SwissSidechain: a molecular and structural database of non-natural sidechains

Gfeller D, Michielin O, Zoete V; Nucleic Acids Research, 41, D327-D332 (2013)

http://www.swisssidechain.ch/data/Gfeller_2013_1.pdf

As a first approximation I use the DREIDING like force field with the potential derived charges in such a situation. For many tasks such simple parameterization enough. Parameterization takes several tens of minutes. Estimates of the energy can be carried out in the GB model. All of this can be done in Abalone.

http://www.biomolecular-modeling.com/Abalone/index.html

Yes, the suite Schrödinger has several software to perform mutation and the incorporation of unnatural amino acids. To study the folding and the Binding free energy you can use Desmond (molecular simulation free software). 

Thanks for all your answers. I am going to look into it.

I previously used FoldX to calculate binding energies for different mutations, but it only mutated 20 natural and 4 modified aa.