Dear Amber users,
I am using 'MMPBSA.py' for calculating the binding free energy of
protein-ligand interaction. But the calculated binding free energy by GB
and PB method shows a large difference (please see the results below) and
I am a bit confused about which method really give significant result.
Unfortunately, I don’t have any experimental data to compare with.
*
MMGBSA*
**************************************************************************************************
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -68.5498 3.3641
0.4758
EEL -9.0344 3.7616
0.5320
EGB 45.6452 3.8693
0.5472
ESURF -7.6578 0.1943
0.0275
DELTA G gas -77.5842 4.6776
0.6615
DELTA G solv 37.9874 3.8488
0.5443
DELTA TOTAL *-39.5968* 4.1714
0.5899
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
***************************************************************************************************
*MMPBSA*
***************************************************************************************************
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -68.5498 3.3641
0.4758
EEL -9.0344 3.7616
0.5320
EPB 32.4824 3.6040
0.5097
ENPOLAR -50.0504 1.0205
0.1443
EDISPER 88.3701 1.0951
0.1549
DELTA G gas -77.5842 4.6776
0.6615
DELTA G solv 70.8021 4.0175
0.5682
DELTA TOTAL *-6.7821* 3.9336
0.5563
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
**************************************************************************************************
Thanks in advance
regards,
Anu
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Received on Sun Aug 25 2013 - 23:30:02 PDT
