Is it possible to run MD simulations of the protein in a complex with an ssDNA?

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Justin Lemkul

Certainly it is possible.

I don't know that anyone has optimized a force field for ssDNA (probably nonexistent target data), so I would imagine your best bet is a high-quality dsDNA force field.

Grzegorz Wieczorek

It seems that people try to do it with the amber ff. Take a look at http://arxiv.org/abs/1207.5145 .