Dear Prof. Case,
Thank you very much. We will check our results and try under different conditions, including with or without magnesium.
Best,
Yufeng
At 2013-04-27 18:57:13,"David A Case" <case.biomaps.rutgers.edu> wrote:
>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 - 17:30:03 PDT
