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

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Mon Jul 3 10:20:15 CEST 2017

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
LJ-SR:161TYR-Protein_B     -49.535        1.5    10.2926    2.73416
Coul-14:161TYR-Protein_B          0          0          0          0
LJ-14:161TYR-Protein_B    -1.20657      0.088   0.533195   0.474622

where Protein_B is the other protein in the complex. I have following
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.

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?

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"
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

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