You always have to neutralize your system.
Also pay attention on the protocol to minimize the DNA, otherwise the double
strands will repel each other and break the hydrogen bonds.
I suggest you to follow the protocol of this paper below, or adapt it for
your implicit solvent system: J. Am. Chem. Soc. 1997, 119, 7463-7469
I hope I was helpful
On Fri, Aug 12, 2011 at 7:27 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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--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Fri Aug 12 2011 - 16:30:02 PDT
