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?
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.
3). What is the EGB energy? what is ESURF energy?
4). Is delt_G_solv - delt_G_gas the solvent energy?
Thank you very much!
Laura
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Received on Tue Nov 22 2022 - 07:00:02 PST
