[gmx-users] Energy analysis

[Amir Zeb]

Thanks Mark,

Depends what you mean by "stability."
Actually, I don't know the role of metal ion if it is used as co-factor by
a particular protein. I thought to do comparative analysis by MD simulation
which might predict the possible role of metal (in this case Zn^2+). Other
analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
already done, but I want to get insight in their energetic terms while
addressing the question why such changes occurred?
According to the best of my study, there is no experimental data available
for my target protein and that's why I want to predict its free-energy of
folding or whatever else.
Will you kindly suggest me some hand notes or tutorial like to do
free-energy analysis for both the systems; means a) protein with metal ion
and b) protein without metal ion?

Amir

On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Depends what you mean by "stability." A well designed study could seek to
> measure or estimate the difference in the free-energy of folding, but that
> would probably require an infeasibly large amount of sampling, and be
> highly dependent on the quality of the parameterization of the
> metal-protein interactions, for which you would probably need some suitable
> experimental data.
>
> Mark
>
> On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb <zebamir85 at gmail.com> wrote:
>
> > Hi gromacs users,
> >
> > I want to calculate the energy for comparative analysis of protein with
> and
> > without metal ion, wherein I would like to determine the influence of
> metal
> > on protein structural stability. I have used gromacs for simulation.
> Please
> > suggest me how to do this kind of analysis? Should i follow a specific
> > tutorial?
> >
> > Amir
> > --
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