Hi Ashwini,
On 21/03/2012, at 11:33 PM, ashwini gupta <wini657.gmail.com> wrote:
> Dear Ben,
>
> Yes it is. :)
>
> So, while preparing the prmtop and inpcrd file I essentially fix the water
> molecule that coordinates with metal by naming it as MOH while the other
> water molecules are name ad HOH. Is this correct. shouldn't the water
> molecules move ard and different water molecules interact with the metal at
> different time points. Will the two things mean the same?
If you want to model a situation in which one water molecule dissociates from the metal ion and is replaced by another, then you probably don't want to use MCPB at all. MCPB uses a "bonded force field" approach, and assumes an unchanging coordination environment around the metal. If you hope to change the coordination environment, you'll need to use a non-bonded complex model, or else treat the metal centre quantum-mechanically.
Best,
Ben
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Received on Wed Mar 21 2012 - 04:00:03 PDT
