[gmx-users] Energy analysis

[Justin Lemkul]

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.warren at 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.warren at 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 <zebamir85 at 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.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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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jalemkul at vt.edu | (540) 231-3129
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