On Sat, Apr 27, 2013, crazylyf.126.com wrote:
>
> Thank you for your advice. The reason we tried to use the ff98 force
> field is that a previous paper ("RNA Stability Under Different
> Combinations of Amber Force Fields and Solvation Models") concluded
> a best performance for RNA simulating combining the ff98 and
> igb1. Currently, we would like to simulate RNAs implicitly, thus ff98 is
> one choice.
OK, but I don't think any of the implicit solvent models are expecting one to
have explicit magnesium ions: in Amber, implicit solvents imply that both the
water and mobile ions are treated implicitly. If you after a "bound" ion,
you'll have to adjust the input files (and carefully check your results).
...dac
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Received on Sat Apr 27 2013 - 04:00:02 PDT
