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标题: 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 [打印本页]

作者
Author: H.J.Zhao 时间: 2024-3-11 10:28
标题: 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
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
|
|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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