[gmx-users] protein protein interaction: side chain contribution

Justin Lemkul jalemkul at vt.edu
Wed Jul 5 14:50:25 CEST 2017

On 7/3/17 4:20 AM, Tushar Ranjan Moharana wrote:
> Hi all,
> I want to know the contribution of various amino acid side chain in complex
> that composed of 2 proteins. I used GROMOS53a6 forcefiel for the
> simulation. All parameters are as recommended by the concerned paper. I
> made separate index groups for each amino acid side chain and the proteins.
> I calculated Coulomb and LJ interaction using gmx energ between the amino
> acid and the interacting protein. Following are few results, I obtained:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ------------------------------------------------------------
> -------------------
> Coul-SR:161TYR-Protein_B   -74.0397        1.9    17.8364    8.11782
> (kJ/mol)
> LJ-SR:161TYR-Protein_B     -49.535        1.5    10.2926    2.73416
> (kJ/mol)
> Coul-14:161TYR-Protein_B          0          0          0          0
> (kJ/mol)
> LJ-14:161TYR-Protein_B    -1.20657      0.088   0.533195   0.474622
> (kJ/mol)
> where Protein_B is the other protein in the complex. I have following
> doubts.
> 1) Energy I obtained looks too high to me. Is everything correct? I
> searched for information but couldn't get much, so don't know what should
> be the ideal values. Results might be correct but I am not sure.

I don't know how you're making this assessment.  Your numbers look to be of 
reasonable magnitude, though I'm not sure how you have a 1-4 term between 
different protein units.  Check your index groups.

> 2) How can I calculate kinetic energy of the amino acid side chain? gmx
> traj or energy(after saving only desired atoms in the trajectory) which one
> will be more meaning full?

You can do it either way, but I would argue that neither is actually meaningful.


> Kindly help me at least in the first question. Any kind of
> informations/suggestions are most welcom.
> Thanks for your valuable time and efforts.
> "A society with free knowledge is better than a society with free food"


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


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