See my responses below. Hope they help.
-Bill
On Tue, Nov 22, 2022 at 8:52 AM laura zhang via AMBER <amber.ambermd.org>
wrote:
> Dear all,
>
> I used MMPBSA.py program to calculate the binding energy between a
> molecule and a protein. In the mmgbsa_perframe.dat file, it has the
> following content (only the first 3 rows of output were pasted):
>
> DELTA Energy Terms
> Frame #,VDWAALS,EEL,EGB,ESURF,DELTA G gas,DELTA G solv,DELTA TOTAL
>
> 0,-30.189999999999916,-5.574600000000572,16.03809999999998,-3.763170720000006,-35.78730000000145,12.27492927999991,-23.512370720001556
>
> 1,-31.88460000000009,-1.8694999999998458,15.042999999999868,-3.7068357599999997,-33.74270000000064,11.336164239999881,-22.40653576000122
>
> 2,-35.318800000000024,-3.8298000000000556,19.04240000000012,-3.852056159999998,-39.19859999999909,15.190343840000073,-24.00825615999878
>
> I have the following questions:
> 1). Here, the last column (8th column) should be the delt_G_binding data
> we need, is that right?
>
Yes, the last column should be the binding free energy in kcal/mol.
> 2). When I added the 2nd to 7th items together, I did not get the same
> value as the 8th one. After I divided the sum of the 2nd to 7th items by 2,
> I got the 8th item. I am wondering what is the reason for that.
>
VDWAALS (column 2) and EEL (column 3) add to the DELTA G gas (column 6)
value. And EGB (column 4) and ESURF (column 5) sum to the DELTA g solv
(column 7). And then DELTA G gas (column 6) and DELTA g solv (column 7)
should sum to the DELTA TOTAL (column 8). So the numbers are double up, but
on purpose so you can see the breakdown of energy values.
> 3). What is the EGB energy? what is ESURF energy?
>
EGB refers to the polar solvation free energy term. And ESURF corresponds
to the nonpolar solvation free energy term.
> 4). Is delt_G_solv - delt_G_gas the solvent energy?
>
The solvation free energy (as mentioned above) is the sum of EGB and ESURF.
>
> Thank you very much!
>
> Laura
>
>
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--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Tue Nov 22 2022 - 10:30:02 PST
