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 Fri Aug 12 2011 - 15:30:03 PDT
