Hi Shreeramesh,
In AmberTools16, the recommended divalent ion parameters can be loaded together with the specific water model through the water model cmd files (with names as leap.water.* ). However, as Dave said, it is challenging to model divalent ions accurately. You can try the 12-6-4 model if interested, which may offer improved results than the 12-6 model. Here is a tutorial for modeling ions in AMBER: http://ambermd.org/tutorials/advanced/tutorial20/ <http://ambermd.org/tutorials/advanced/tutorial20/>.
Kind regards,
Pengfei
> On May 30, 2016, at 9:19 AM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, May 30, 2016, Shreeramesh wrote:
>>
>> I have to run MD simulation in AMBER for the protein-DNA system comprising
>> magnesium ion.
>>
>> Can you please guide me how to treat magnesium ion in the complex?
>
> Please see the "ions" section in section 3.6 of the Amber 2016 Reference
> Manual. The parameters for ions are tightly coupled with which water model
> you choose. In AmberTools16, we have simplified things quite a bit: if you
> choose a water model (by loading a leaprc.water.* file), you automatically get
> our recommended parameters for monatomic ions.
>
> Aside: divalent ions are difficult to simulation, so advanced users may wish
> to explore other combinations of parameters.
>
> ...good luck....dac
>
>
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Received on Tue May 31 2016 - 08:00:02 PDT
