

i am currently doing something similar to what you are suggesting and I find that Amber is quit capable of dealing with these mutations

It is possible to change single residues in the link stage ie remove charge etc

or even mutate the residue using WHATIF see Gert Vriend Heidleberg EMBL

I do not have a full set of results yet but they look promising

So in answer to your question Amber MD is quite sufficient
Please mail me if you have any other ideas/questions 
[email-masked]

byee
Paul