Dear Amber users
I obtained positive free energy from mmpbsa.py.
In my case the receptor and ligand didn't joint together. The distance between them
is about 1-2 angstrom. Is this related to positive free energy?
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -411.6759 1.7294 0.0141
EEL 569.3971 6.2254 0.0508
EPB -201.2496 1.3530 0.0110
ENPOLAR 454.9821 0.5963 0.0049
EDISPER -736.8974 4.8014 0.0392
G gas 157.7212 6.4945 0.0530
G solv -483.1649 5.2294 0.0427
TOTAL -325.4437 8.1389 0.0665
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -365.5924 0.9813 0.0080
EEL 295.2994 1.7603 0.0144
EPB -186.0528 0.8477 0.0069
ENPOLAR 434.0409 0.4641 0.0038
EDISPER -569.1774 1.2950 0.0106
G gas -70.2931 2.1282 0.0174
G solv -321.1893 1.6779 0.0137
TOTAL -391.4823 2.1113 0.0172
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 3.9950 0.9566 0.0078
EEL 275.2529 5.8769 0.0480
EPB -22.5611 0.9193 0.0075
ENPOLAR 43.1728 0.1163 0.0009
EDISPER -522.6284 2.1411 0.0175
G gas 279.2479 5.9180 0.0483
G solv -502.0167 2.3545 0.0192
TOTAL -222.7687 6.8139 0.0556
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -50.0785 1.0295 0.0084
EEL -1.1552 0.3301 0.0027
EPB 7.3643 0.8011 0.0065
ENPOLAR -22.2317 0.3450 0.0028
EDISPER 354.9084 4.6963 0.0383
DELTA G gas -51.2337 1.1193 0.0091
DELTA G solv 340.0410 4.9708 0.0406
DELTA TOTAL 288.8073 4.6026 0.0376
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Z. Khatti, Ph.D student of Physical Chemistry,
Department of Chemistry, Iran University of Science & Technology,Tehran, Iran
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Received on Wed Aug 20 2014 - 11:30:02 PDT
