[gmx-users] g_lie query

[Anirban Ghosh]

Thanks Justin for the reply.
I have through the threads about g_lie, but cannot understand how to get the
values for Elj and Eqq for a particular ligand. Like in my case for a system
consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what
should be the values for Elj and Eqq?

Thanks a lot.

Anirban

On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hi ALL,
>>
>> I have run a protein + ligand (dopamine) simulation. Now I want to
>> calculate the free energy of binding using g_lie. But g_lie asks for two
>> values: Elj and Eqq. How or from where can I get these values for my ligand?
>> Also, do I need to run a simulation with only the ligand? And, is there any
>> other way (like MMGBSA in Amber) to calculate the free energy for my
>> simulation? Any suggestion is welcome.
>> Thanks a lot in advance.
>>
>>
> Go to the literature and understand what information is needed for such a
> simulation, and then look into the list archives and you'll find dozens of
> threads about using g_lie.
>
> -Justin
>
>
>> Regards,
>>
>> Anirban
>>
>>
> --
> ========================================
>
> 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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