Hi Asmi,
I have recently been working on this and I am still in the testing phase, but these files (attached) should make it possible to use the Allner et al. parameters you are referring to.
To make sure you are using these new parameters, you may want to comment out these lines below in "amber11/dat/leap/parm/parm10.dat" or the equivalent lines in amber12 and whatever force field you are using. You may not have to do this, but I did just to make sure.
MG 24.305 0.120 magnesium
...
MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
Let me know how it works out.
Best regards,
Jesper
On May 16, 2012, at 11:01 AM, Asmita Gupta wrote:
> Dear Users,
>
> I want to run a simulation on RNA in presence of Mg ions. As of Amber12,
> the parameter set for Mg+ are rather old defined by Aqvist et.al (1990).
> While recently new Mg+ parameters sets have been defined by Villa
> et.al.(2012) (Ref : Magnesium Ion water coordination and exchange in
> biomolecular simulations). I want to know is there any way by which i can
> use these new parameters with Amber12. What modifications i'll have to do
> for this implementation and how?
>
> Thanks
>
> Asmi..
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Received on Wed May 16 2012 - 12:00:03 PDT
