Re: [AMBER] Query regarding the internal energy of protein.

From: Pratul Agarwal <>
Date: Mon, 17 Dec 2018 15:37:58 +0000

I agree with previous mail, there is no correct way of doing this. If you are strictly looking for computing the sum of protein's internal energy terms and MM-PBSA or MM-GBSA does not provide what you are looking for, then here is another but longer way (requiring significantly more effort):
1. Create a topology file for the protein only.
2. From your explicit simulations, if you stored the coordinates, extract frames and strip away water. Store them as restart files.
3. Using protein only topology from step #1 and each frame in #2, run an MD (or minimization) for 1 step. The results for time=0 will have the terms for protein internal energy.
4. You can automate this protein for multiple frames using a script.

Caveat emptor: Energy terms at step 1 and beyond will be wrong and meaningless as protein has gone from solvated condition to vacuum (or another implicit solvent if you use one).

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 12/17/2018 5:09 AM, Leena Aggarwal wrote:

Dear Amber Users

I have run the explicit water MD simulation of a protein. I want to
calculate the internal energy of protein from the total energy of the
system which is given as:

Total energy = configurational energy of protein+ protein-solvent
interaction energy + solvent-solvent interaction energy.

Total energy=Ebond + Eangle + Edihedral + E1-4NB + E1-4EEL + EVDWAALS+ EElec

I have got the total energy of the system at each step from the output
files generated during the simulation. In this, the last two terms i.e
Lennard Jones and Electrostatic interaction terms include contributions
from solute-solvent and solvent-solvent interaction energy also.

Any suggestions for calculating the configurational energy of protein from
total energy of the system.
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Received on Mon Dec 17 2018 - 08:00:03 PST
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