Hi,
If you are doing implicit solvent simulations adding explicit
counterions may not be a good idea. For one thing, (to my knowledge)
the ion parameters are not designed or optimized for use with any of
the implicit solvent models available in Amber.
This is just my opinion, but I think in the case of implicit solvation
a better idea is to set the salt concentration (saltcon for GB, istrng
for PB I think). If you want to use explicit counterions you should
probably also use an explicit solvent model.
-Dan
On Fri, Aug 12, 2011 at 6:27 PM, manikanthan bhavaraju
<manikanthanbhavaraju.gmail.com> wrote:
> Dac I am using ff99SB forcefield.
>
> But I have a question regarding the DNA and DNA + ligand implicit solvations
> simulations.
>
> When we are preparing prmtop and inpcrd files in both cases, Do we have to
> add counterions ? In my case the DNA has -22 charge and ligand +1. Can
> counterions stablize the simulations?
>
> I am not sure whether I have to add counterions or not. Please suggest me.
>
> Thanks,
> mani
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Received on Sat Aug 13 2011 - 06:00:04 PDT
