[gmx-users] Regarding simulation analysis and free energy calculation

[Justin Lemkul]

On 8/10/14, 3:56 AM, rama david wrote:
> Dear users,
>                     I did the docking of peptide and receptor in Vina
> autodock.
> further I decided to do the simulation in gromacs. 4.5.5 version for 10ns.
> after this I made the energygroups in mdp file for ligand and and receptor.
> I also make the appropriate changes in index file. I rerun the above
> simulation again.
>
> Now I want to do the following analysis . I will be thankful if you suggest
> how to do analysis  and suggestion .
>
> 1.  I want to calculate the hydrogen bond --- I used g_hbond.
>
> 2. Now I want to find the interaction energy of ligand and receptor .
>     How to do that ???
>

It's already in the .edr file if you used appropriate energygrps.  Now, whether 
or not that quantity has any physical meaning is another issue.

> 3. Is it possible to calculate free enegy of interaction between ligand and
> receptor ?
>      how to do this ?
>

Free energy of binding between ligands and receptors is straightforward. 
Consult the ample amount of literature on this topic.

> 4. I want to make the graph with respect to free energy surface  and
> ligand
>       conformation.? How to do this ?
>

It's not something Gromacs can do.  Internal energy is easy, but entropy is not.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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