Dear Amber users,
I calculated the binding free energy and free energy decomposition per
residue (idecompose 2) for a protein-dna system.
Binding free energy MMGBSA values looks like this
VDWAALS -52.8546 3.1674
0.1002
EEL -61.9466 9.5779
0.3029
EGB 74.6023 8.5019
0.2689
ESURF -6.7388 0.1845
0.0058
DELTA G gas -114.8011 9.7739
0.3091
DELTA G solv 67.8634 8.4739
0.2680
DELTA G binding = -46.9377 +/- 3.2026
0.1013
Total Free energy decomposition looks like this
DT5 1 | L DT5 1 | 0.000 +/- 5.511 | -15.496 +/- 2.153 |
-10.790 +/- 3.306 | 16.087 +/- 2.644 | -2.215 +/- 0.058 |
-12.415 +/- 7.276
DC3 2 | L DC3 2 | 0.000 +/- 6.159 | -10.931 +/- 2.366 |
-20.183 +/- 5.474 | 29.037 +/- 4.123 | -1.828 +/- 0.078 |
-3.905 +/- 9.513
ASP 3 | R ASP 1 | 0.000 +/- 3.568 | -0.005 +/- 2.073 |
-1.488 +/- 8.387 | 1.591 +/- 8.205 | 0.000 +/- 0.148 |
0.097 +/- 12.439
ILE 4 | R ILE 2 | 0.000 +/- 4.338 | -0.013 +/- 2.225 |
-0.019 +/- 3.006 | 0.022 +/- 1.788 | 0.000 +/- 0.080 |
-0.010 +/- 6.000
LEU 5 | R LEU 3 | 0.000 +/- 3.965 | -0.003 +/- 1.702 |
0.104 +/- 1.652 | -0.095 +/- 0.801 | 0.000 +/- 0.085 |
0.006 +/- 4.690
MET 6 | R MET 4 | 0.000 +/- 3.812 | -0.006 +/- 1.602 |
0.017 +/- 1.658 | -0.013 +/- 1.165 | 0.000 +/- 0.051 |
-0.002 +/- 4.605
THR 7 | R THR 5 | 0.000 +/- 3.515 | -0.001 +/- 1.658 |
0.105 +/- 2.800 | -0.100 +/- 1.499 | 0.000 +/- 0.086 |
0.004 +/- 5.020
I have a doubt regarding these values. I assume the sum of the two
ligands (DT5 and DC3) must be equal to the total binding free energy.
Also the sum of the contributions from the different resdiues in the
receptor mask should be equal to the total BE.
If the previous statement is wrong, I assume the decomposition gives
the contribution from the different residues (including both ligand
and receptor) to the binding free eenrgy. But since the binding free
energy is calculated with respect to ligand and receptor, how we can
decompose ligand contribution and receptor residue contribution
seperately? how does the per residue pair basis works then?
Pls give me a clear explanation as the manual doesnt talk anything on
these
Thanks
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Received on Wed Aug 24 2011 - 16:30:02 PDT
