> I am trying to simulate a protein-DNA complex. But I have some problems
> to set up a water box with physiological salt concentration. Some of the
> ions are placed outside of the box during the grid calculation. In a
> periodic boundary simulation, these ions would lie in another box and
> probably overlap there with some water molecules or even the solute of
> this box. What is going wrong here and how can I fix this?
Did you try running sander to see what actually happens?
It may be that you will be lucky.
> The strange thing is that the same input worked pretty fine with amber8.
> solvateoct TAQ TIP3PBOX 12
> addions TAQ Na+ 66 Cl- 44
It is odd that you are adding 12A of water before addIons, in
which case one would expect the ions to replace waters. I wonder
if the code has been changed.
Bill
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Received on Fri Jul 09 2010 - 10:00:04 PDT
