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各位老师好，利用Amber18中MMPBSA.py计算的结合自由能数值发现偏小，请问导致结果异常的原因是什么，下面是具体的输出结果：
Run on Sun Mar 12 12:14:17 2000
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|Input file:
|--------------------------------------------------------------
|&general
| startframe=1, endframe=2500, verbose=1, interval=1, keep_files=2
|# entropy=1,
|/
|&gb
| igb=1, saltcon=0.150, surften=0.0072, surfoff=0.00
|/
|&pb
| istrng=0.150, exdi=80, indi=1.0,
| inp=1, radiopt=0, cavity_surften=0.00542, cavity_offset=0.9200,
| fillratio=4, scale=2.0,
| linit=1000, prbrad=1.4,
|/
|#&nmode
|# nmstartframe=1, nmendframe=2500, nminterval=1, nmode_istrng=0.150 ,maxcyc=30000,
|#/
|&decomp
| idecomp=2, print_res="1-225"
| dec_verbose=3,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: ../model2_solvated.prmtop
|Complex topology file: ../model2.prmtop
|Receptor topology file: ../hTNFR1.prmtop
|Ligand topology file: ../apt1_2.prmtop
|Initial mdcrd(s): ../mmpbsa_model2_prod26_30_2500frame.nc
|
|Receptor mask: ":1-158"
|Ligand mask: ":159-225"
|
|Calculations performed using 500 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
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 1011.2404 25.2402 1.1288
ANGLE 2424.0779 37.2221 1.6646
DIHED 3580.7018 23.3562 1.0445
VDWAALS -2280.8951 22.7368 1.0168
EEL 11149.8901 271.9239 12.1608
1-4 VDW 1081.2805 13.5607 0.6065
1-4 EEL -511.4215 45.1524 2.0193
EGB -32964.6868 267.1309 11.9465
ESURF 155.8808 1.3731 0.0614
G gas 16454.8742 273.7797 12.2438
G solv -32808.8060 267.0236 11.9417
TOTAL -16353.9318 47.1408 2.1082
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 61308.7571 8324.7035 372.2921
ANGLE 1762.3919 124.0562 5.5480
DIHED 2079.4412 18.5657 0.8303
VDWAALS -1000.8828 16.2591 0.7271
EEL -11152.4243 79.8184 3.5696
1-4 VDW 514.4356 9.3741 0.4192
1-4 EEL 6446.0453 36.4174 1.6286
EGB -2143.6284 63.3649 2.8338
ESURF 78.1269 1.2676 0.0567
G gas 59957.7640 8392.9764 375.3453
G solv -2065.5015 62.8204 2.8094
TOTAL 57892.2624 8380.4603 374.7856
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 552.2465 19.4915 0.8717
ANGLE 1183.0491 26.2130 1.1723
DIHED 1612.9679 15.6148 0.6983
VDWAALS -1208.1067 14.6974 0.6573
EEL 22734.9342 215.2702 9.6272
1-4 VDW 565.9700 8.9247 0.3991
1-4 EEL -6983.1237 27.0748 1.2108
EGB -31275.6115 213.4474 9.5457
ESURF 85.3708 0.5625 0.0252
G gas 18457.9373 211.4835 9.4578
G solv -31190.2407 213.5424 9.5499
TOTAL -12732.3034 32.8998 1.4713
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -60849.7631 8324.4884 372.2824
ANGLE -521.3631 122.1235 5.4615
DIHED -111.7073 9.7654 0.4367
VDWAALS -71.9056 5.4264 0.2427
EEL -432.6198 113.2432 5.0644
1-4 VDW 0.8749 0.2936 0.0131
1-4 EEL 25.6569 0.8179 0.0366
EGB 454.5531 112.1099 5.0137
ESURF -7.6168 0.6247 0.0279
DELTA G gas -61960.8271 8373.2742 374.4642
DELTA G solv 446.9363 112.0051 5.0090
DELTA TOTAL -61513.8908 8376.7313 374.6188
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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 1011.2404 25.2402 1.1288
ANGLE 2424.0779 37.2221 1.6646
DIHED 3580.7018 23.3562 1.0445
VDWAALS -2280.8951 22.7368 1.0168
EEL 11149.8901 271.9239 12.1608
1-4 VDW 1081.2805 13.5607 0.6065
1-4 EEL -511.4215 45.1524 2.0193
EPB -33006.6944 268.9999 12.0300
ENPOLAR 127.5389 1.0119 0.0453
G gas 16454.8742 273.7797 12.2438
G solv -32879.1554 268.9892 12.0296
TOTAL -16424.2813 51.2154 2.2904
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 61308.7571 8324.7035 372.2921
ANGLE 1762.3919 124.0562 5.5480
DIHED 2079.4412 18.5657 0.8303
VDWAALS -1000.8828 16.2591 0.7271
EEL -11152.4243 79.8184 3.5696
1-4 VDW 514.4356 9.3741 0.4192
1-4 EEL 6446.0453 36.4174 1.6286
EPB -2131.8979 65.0086 2.9073
ENPOLAR 65.7689 0.8677 0.0388
G gas 59957.7640 8392.9764 375.3453
G solv -2066.1290 64.6941 2.8932
TOTAL 57891.6349 8379.5621 374.7454
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 552.2465 19.4915 0.8717
ANGLE 1183.0491 26.2130 1.1723
DIHED 1612.9679 15.6148 0.6983
VDWAALS -1208.1067 14.6974 0.6573
EEL 22734.9342 215.2702 9.6272
1-4 VDW 565.9700 8.9247 0.3991
1-4 EEL -6983.1237 27.0748 1.2108
EPB -31353.0632 211.3330 9.4511
ENPOLAR 70.0171 0.5714 0.0256
G gas 18457.9373 211.4835 9.4578
G solv -31283.0461 211.4946 9.4583
TOTAL -12825.1088 32.3152 1.4452
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -60849.7631 8324.4884 372.2824
ANGLE -521.3631 122.1235 5.4615
DIHED -111.7073 9.7654 0.4367
VDWAALS -71.9056 5.4264 0.2427
EEL -432.6198 113.2432 5.0644
1-4 VDW 0.8749 0.2936 0.0131
1-4 EEL 25.6569 0.8179 0.0366
EPB 478.2668 113.9810 5.0974
ENPOLAR -8.2471 0.4357 0.0195
EDISPER 0.0000 0.0000 0.0000
DELTA G gas -61960.8271 8373.2742 374.4642
DELTA G solv 470.0197 113.8826 5.0930
DELTA TOTAL -61490.8074 8372.8420 374.4449
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发表于 Post on 2024-3-11 10:28:24
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