On 11/20/17 1:09 AM, Amir Zeb wrote:
Yes Dr. Dallas,
I have gone through free energy analysis tutorial, But I'm wondering that
whether this tutorial is working for large molecule like protein or not?
Because the tutorial has explained methane only.
No, that tutorial is not relevant nor should anyone try to decouple an
entire protein like that. It's an exercise in futility.
You want to determine the change in folding free energy of an entire
protein based on only the presence of a single ion? I doubt that's even
possible by MD simulations, at least not with any degree of reliability.
-Justin
Your feedback will highly be appreciated.
Thanks!
Amir
On Sun, Nov 19, 2017 at 5:54 PM, Dallas Warren <dallas.war...@monash.edu>
wrote:
Always a good starting point ....
http://www.gromacs.org/Documentation/Tutorials
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
On 20 November 2017 at 12:34, Amir Zeb <zebami...@gmail.com> wrote:
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.abra...@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 <zebami...@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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