Hi Abhilash,
Do you want to model all the 6 coordination bonds with the bonded model?
-Pengfei
> On May 31, 2018, at 12:45 PM, Abhilash J <md.scfbio.gmail.com> wrote:
>
> Hi everyone,
>
> I plan on simulating a ADP with one MG2+ion and protein.
> Will it be plausible to take a Mg2+ with 6 co-ordinate bonds. Three with
> Oxygen atoms of ADP (in the phosphates) and three with oxygen atoms in
> water molecules (Octahedral form).
> I can parameterize this using MCPB.py or Gaussian to get a bonded or a
> non bonded model to run simulation in it.
> I don't want to keep bonds with the protein as i need to study the
> dissociation of ADP from the protein.
> Is the ADP + MG2 + 3 water in Octahedral form configuration a reasonable
> assumption for a starting structure.
>
>
> Regards
>
> Abhilash
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Received on Sat Jun 02 2018 - 15:30:02 PDT
