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各位老师好，我使用Amber的MMPBSA.py计算蛋白质配体复合物的结合自由能，1.计算GB时 算出来的结合自由能比较正常，但是计算的PB是正值，这是不是有一定问题呢？
2.计算PB时，我只修改了离子强度为0.150，其他采用默认值，其中indi（内部介电常数）默认为1，我发现有说法说内部介电常数对于计算MMPBSA有影响，我是不是应该对他进行一定的修改？
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 1464.4089 30.7236 3.0724
ANGLE 4230.0917 52.2753 5.2275
DIHED 6237.1843 26.3400 2.6340
VDWAALS -4160.8411 27.2849 2.7285
EEL -33597.1878 133.7677 13.3768
1-4 VDW 1810.4365 18.3126 1.8313
1-4 EEL 20058.7265 43.1286 4.3129
EGB -6319.8715 131.6967 13.1697
ESURF 168.7644 2.8871 0.2887
G gas -3957.1810 159.3133 15.9313
G solv -6151.1071 129.7379 12.9738
TOTAL -10108.2881 67.9293 6.7929
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 1455.9050 30.4318 3.0432
ANGLE 4199.6123 51.7239 5.1724
DIHED 6214.3463 26.2133 2.6213
VDWAALS -4141.0254 27.4628 2.7463
EEL -33574.4530 132.6165 13.2617
1-4 VDW 1797.8812 18.0330 1.8033
1-4 EEL 20086.4756 43.0982 4.3098
EGB -6331.4824 131.7796 13.1780
ESURF 168.7339 3.0005 0.3000
G gas -3961.2581 158.8286 15.8829
G solv -6162.7485 129.6828 12.9683
TOTAL -10124.0066 67.1412 6.7141
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 8.5039 2.4291 0.2429
ANGLE 30.4793 4.0228 0.4023
DIHED 22.8411 1.6620 0.1662
VDWAALS -1.4264 1.0825 0.1082
EEL -2.0698 0.7446 0.0745
1-4 VDW 12.5553 1.2581 0.1258
1-4 EEL -27.7490 0.8816 0.0882
EGB -13.2949 0.3790 0.0379
ESURF 2.7373 0.0136 0.0014
G gas 43.1345 4.7239 0.4724
G solv -10.5576 0.3737 0.0374
TOTAL 32.5769 4.6240 0.4624
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0000 0.0000
ANGLE 0.0000 0.0000 0.0000
DIHED -0.0031 0.0094 0.0009
VDWAALS -18.3893 2.9492 0.2949
EEL -20.6650 4.5937 0.4594
1-4 VDW 0.0000 0.0000 0.0000
1-4 EEL 0.0000 0.0000 0.0000
EGB 24.9057 2.6494 0.2649
ESURF -2.7067 0.2866 0.0287
DELTA G gas -39.0574 3.7641 0.3764
DELTA G solv 22.1990 2.6780 0.2678
DELTA TOTAL -16.8584 2.0937 0.2094
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 1464.4089 30.7236 3.0724
ANGLE 4230.0917 52.2753 5.2275
DIHED 6237.1843 26.3400 2.6340
VDWAALS -4160.8411 27.2849 2.7285
EEL -33597.1878 133.7677 13.3768
1-4 VDW 1810.4365 18.3126 1.8313
1-4 EEL 20058.7265 43.1286 4.3129
EPB -5772.3062 121.6906 12.1691
ENPOLAR 3733.8246 12.5317 1.2532
EDISPER -1906.4560 12.2418 1.2242
G gas -3957.1810 159.3133 15.9313
G solv -3944.9376 120.8963 12.0896
TOTAL -7902.1186 75.8495 7.5850
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 1455.9050 30.4318 3.0432
ANGLE 4199.6123 51.7239 5.1724
DIHED 6214.3463 26.2133 2.6213
VDWAALS -4141.0254 27.4628 2.7463
EEL -33574.4530 132.6165 13.2617
1-4 VDW 1797.8812 18.0330 1.8033
1-4 EEL 20086.4756 43.0982 4.3098
EPB -5785.5219 122.7910 12.2791
ENPOLAR 3717.4175 13.1540 1.3154
EDISPER -1903.4604 12.9531 1.2953
G gas -3961.2581 158.8286 15.8829
G solv -3971.5647 122.1137 12.2114
TOTAL -7932.8228 74.6569 7.4657
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 8.5039 2.4291 0.2429
ANGLE 30.4793 4.0228 0.4023
DIHED 22.8411 1.6620 0.1662
VDWAALS -1.4264 1.0825 0.1082
EEL -2.0698 0.7446 0.0745
1-4 VDW 12.5553 1.2581 0.1258
1-4 EEL -27.7490 0.8816 0.0882
EPB -13.7456 0.2847 0.0285
ENPOLAR 32.8441 0.1676 0.0168
EDISPER -31.7904 0.1690 0.0169
G gas 43.1345 4.7239 0.4724
G solv -12.6920 0.3811 0.0381
TOTAL 30.4425 4.7121 0.4712
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0000 0.0000
ANGLE 0.0000 0.0000 0.0000
DIHED -0.0031 0.0094 0.0009
VDWAALS -18.3893 2.9492 0.2949
EEL -20.6650 4.5937 0.4594
1-4 VDW 0.0000 0.0000 0.0000
1-4 EEL 0.0000 0.0000 0.0000
EPB 26.9613 3.9262 0.3926
ENPOLAR -16.4370 1.6003 0.1600
EDISPER 28.7947 1.9437 0.1944
DELTA G gas -39.0574 3.7641 0.3764
DELTA G solv 39.3191 4.1325 0.4133
DELTA TOTAL 0.2617 3.6693 0.3669
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mmpbsa.dat
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结合自由能的计算
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发表于 Post on 2022-8-22 16:33:32
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