Dear Amber users!
Performing mmgbsa with quasi-harmonic calculations for my receptor-agonist
complex I've obtained very high free energy for typical "good" binder as
the ligand. From the below results you can see that the main unfavorable
contribution (=source of wrong free energy value) came from the enthropy
term calculated here using quasi-harmonic method. Does it means that q-h
calculations always produce bad results in comparison to NMA? Might the
high enthopy be evedence of some problems with input data (e.g not
convergence of the input trajectory)? Are there any imput options for Q-H
which could improve results?
1)Enthalpy
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -27.3927 1.4357
0.1401
EEL -5.2307 2.4454
0.2386
EGB 10.8602 1.5605
0.1523
ESURF -3.4942 0.1079
0.0105
DELTA G gas -32.6234 2.7259
0.2660
DELTA G solv 7.3660 1.5721
0.1534
DELTA TOTAL -25.2574 2.2894
0.2234
2)ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
Translational Rotational Vibrational Total
Complex: 16.9767 17.7092 282.7339 317.4194
Receptor: 16.9725 17.7089 282.4909 317.1720
Ligand: 12.1949 8.8983 16.8228 37.9160
DELTA S: -12.1908 -8.8980 -16.5798 -37.6686
-------------------------------------------------------------------------------
3) Using Quasi-harmonic Entropy Approximation: DELTA G binding = 12.4112
Thanks for help,
James
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Received on Tue Oct 07 2014 - 01:00:02 PDT
