On Mon, Jan 13, 2014, Zhuang, Yu wrote:
>
> I am interested in investigating the interaction between polymers, such
> as protein and protein (with 1500 atoms) using molecular simulation. Do
> you think Amber 12 is a good tool to apply or do your have some
> recommendations regarding it? Thanks in advance.
Amber is generally a good tool for carrying out simulations of proteins in
water. Only you know what you wish to learn by "investigating the
interaction" between proteins. It makes a big difference (for example)
whether or not the proteins are in a native, folded state or not. Or (for a
second example) how much is known in advance about the structures of the
individual chains, and about the strucure of their complexes. Try to find
examples in the literature of calculations similar to those you hope to do.
...good luck...dac
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Received on Mon Jan 13 2014 - 05:30:06 PST
