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[mohsen ramezanpour]

Dear Dr.Justin

I couldn't find any tutorial for doing free energy cycles with gromacs.
Then I was forced to select Umbrella sampling,I read your toturial and it
was very useful for me.I know it approximately good now.
Please let me know if there are any tutorial for free energy cycles.
I want to learn how I can do this.
Thanks in advance for your guidance


On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear All
>>
>> I want to evaluate the binding free energy of protein-dryg.
>>
>> My protein has so many atoms(5000 atoms),it make running too long.
>> I want to use Umbrella sampling for this.
>>
>> Can I separate active site of protein (a radious of 3 nm around of my drug
>> )and do my work on this system?
>>
>
> I would think that such a fractured system would suffer from a number of
> unpredictable artifacts.  Protein structure is fairly sensitive, so you'd
> have to apply lots of artificial restraints to preserve geometry, but then
> what if even small conformational changes are needed to for the protein to
> properly bind the drug?
>
> Umbrella sampling is one of the more laborious ways of calculating binding
> energies.  Free energy cycles would probably be significantly more
> efficient, since you can use a smaller box size and (in all likelihood) run
> shorter simulations that still converge.
>
> -Justin
>
>
>  Thanks in advance for your guidances.
>> Mohsen
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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