Mg2+/GDP does not always have three ADP oxygens in the first shell of Mg2+.
See, for instance, the two highest resolution structures in the PDB with
ADP and Mg2+ (PDBs: 2CNQ and 1KJQ), which each have only 2 direct
ADPoxygen-Mg2+ contacts. Given that the lifetimes of atoms in Mg2+'s first
shell are likely much longer than what you can achieve via simulation, I'd
try to find some experimental evidence for the Mg2+ coordination in your
particular system.
On Sat, Jun 2, 2018 at 4:07 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> 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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>
>
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Received on Sat Jun 02 2018 - 16:30:02 PDT
