[gmx-users] Problem in Free Energy Calculations

[shagun krishna]

Hi Justin,
You mean to say that I don't need to follow your Free Energy Calculations :
Methane in Water.
Actually I want to calculate the binding energy of my ligands with my
protein. All I should do is to run the one simulation of my ligands simply
in water and another is the protein-ligand complex simulation, both for
10ns. I am really very confused because I have gone through literature and
all of them have calculated the value of α, β and  γ, which i guess can be
calculated by using free energy codes.

Regards,

Shagun

On Thu, Dec 31, 2015 at 9:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/31/15 11:19 AM, shagun krishna wrote:
>
>> Hii Justin,
>>
>> I am using the old version of gromacs i.e 4.6.5 and the tutorial that I am
>> following is also compatible with the same version. Then too I am getting
>> the problem.
>>
>>
> If you upgrade to the current version, your life will be a lot easier.
> The 4.6.5 version of the tutorial used some crude scripting to make things
> work; it could be more elegant but I'm afraid I do not have time to
> troubleshoot outdated information.  I intend on taking the old versions of
> the tutorials offline, anyway.
>
> One more thing if I got the energy for the ligand and the protein how would
>> I combine them to single .edr file since gmx lie program uses a single
>> file
>> such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr
>> <http://manual.gromacs.org/online/edr.html> file. and How I will get the
>> values of  Elj, Eqq, Clj, Cqq.
>>
>>
> If you're doing a real free energy calculation, I don't see why you would
> want to do this.  There's plenty of literature out the LIE method, though.
> But it requires two simulations (not using the free energy code):
> protein-ligand and ligand in water.  The interaction energies come from
> energygrps in the .mdp file, so you have everything you need in one .edr
> file; you do not need the energy of the protein and energy of the ligand
> separately.  You need the nonbonded interaction energy between them (as
> well as the ligand-water interaction energy from the second simulation).
>
> -Justin
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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