Thanks Ben :)
On Wed, Mar 21, 2012 at 4:11 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> 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 - 05:00:03 PDT
