[AMBER] positive free energy

From: zahra khatti <zkhatti2000.yahoo.com>
Date: Wed, 20 Aug 2014 11:11:29 -0700

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


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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
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