Thanks David A Case and Pratul Agarwal for the reply.
I have tried the way suggested by Pratul Agarwal and I was able to compute
the protein internal energy from the total energy of the system.
On Mon, Dec 17, 2018 at 9:08 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> 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)
> Web: http://www.agarwal-lab.org/
>
>
> 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 - 22:30:02 PST
