Thank you Prof. Case,
Yes, the bond energy in my calculation is not zero.
I tried to understand what you suggest, so
I performed MMPBSA calculation for one frame, and below is the result.
However, still, I could not figure out what's wrong.
Best regards,
nadaafiva
Result for MMPBSA calculation for one frame
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 4987.7384 14.6855
10.3842
ANGLE 8783.1966 28.4633
20.1266
DIHED 14002.0148 27.6907
19.5803
VDWAALS -8312.5223 12.0942
8.5519
EEL -77073.8675 25.2760
17.8729
1-4 VDW 4093.3003 8.0252
5.6747
1-4 EEL 41943.1001 123.0514
87.0105
EGB -9900.1568 67.0942
47.4428
ESURF 337.1691 0.0760
0.0537
G gas -11577.0396 47.0552
33.2731
G solv -9562.9878 67.0183
47.3891
TOTAL -21140.0274 19.9630
14.1160
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 6474.7614 125.2608
88.5727
ANGLE 8770.3780 49.1306
34.7406
DIHED 13973.9255 29.0412
20.5352
VDWAALS -8283.8561 16.7430
11.8391
EEL -77911.4475 17.1252
12.1094
1-4 VDW 4077.8936 8.3679
5.9170
1-4 EEL 44003.5112 113.3456
80.1475
EGB -9932.5902 66.6209
47.1081
ESURF 338.7891 0.0463
0.0328
G gas -8894.8338 168.4202
119.0911
G solv -9593.8011 66.6672
47.1409
TOTAL -18488.6349 101.7530
71.9502
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 29.2077 4.9909
3.5291
ANGLE 93.0959 3.4445
2.4357
DIHED 41.1711 0.9216
0.6517
VDWAALS -1.6857 1.1140
0.7878
EEL 958.3478 11.8859
8.4046
1-4 VDW 15.2138 0.3411
0.2412
1-4 EEL -2065.3416 9.6983
6.8577
EGB -99.0266 1.5256
1.0787
ESURF 3.6076 0.0107
0.0076
G gas -929.9910 4.2675
3.0176
G solv -95.4190 1.5362
1.0863
TOTAL -1025.4100 2.7313
1.9313
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -1516.2308 134.9554
95.4279
ANGLE -80.2772 17.2227
12.1783
DIHED -13.0818 0.4289
0.3033
VDWAALS -26.9805 3.5347
2.4994
EEL -120.7679 3.7351
2.6411
1-4 VDW 0.1928 0.0016
0.0011
1-4 EEL 4.9305 0.0075
0.0053
EGB 131.4599 1.9989
1.4134
ESURF -5.2275 0.1116
0.0789
DELTA G gas -1752.2148 117.0974
82.8004
DELTA G solv 126.2324 1.8873
1.3345
DELTA TOTAL -1625.9825 118.9847
84.1349
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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 4987.7384 14.6855
10.3842
ANGLE 8783.1966 28.4633
20.1266
DIHED 14002.0148 27.6907
19.5803
VDWAALS -8312.5223 12.0942
8.5519
EEL -77073.8675 25.2760
17.8729
1-4 VDW 4093.3003 8.0252
5.6747
1-4 EEL 41943.1001 123.0514
87.0105
EPB -11008.9913 57.7731
40.8518
ENPOLAR 221.0373 0.3891
0.2752
G gas -11577.0396 47.0552
33.2731
G solv -10787.9541 58.1622
41.1269
TOTAL -22364.9937 11.1070
7.8538
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 6474.7614 125.2608
88.5727
ANGLE 8770.3780 49.1306
34.7406
DIHED 13973.9255 29.0412
20.5352
VDWAALS -8283.8561 16.7430
11.8391
EEL -77911.4475 17.1252
12.1094
1-4 VDW 4077.8936 8.3679
5.9170
1-4 EEL 44003.5112 113.3456
80.1475
EPB -11026.8306 58.4378
41.3218
ENPOLAR 221.6744 0.4101
0.2900
G gas -8894.8338 168.4202
119.0911
G solv -10805.1563 58.8480
41.6118
TOTAL -19699.9901 109.5722
77.4792
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 29.2077 4.9909
3.5291
ANGLE 93.0959 3.4445
2.4357
DIHED 41.1711 0.9216
0.6517
VDWAALS -1.6857 1.1140
0.7878
EEL 958.3478 11.8859
8.4046
1-4 VDW 15.2138 0.3411
0.2412
1-4 EEL -2065.3416 9.6983
6.8577
EPB -113.2438 1.5723
1.1118
ENPOLAR 3.2812 0.0092
0.0065
G gas -929.9910 4.2675
3.0176
G solv -109.9625 1.5632
1.1053
TOTAL -1039.9536 2.7043
1.9123
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -1516.2308 134.9554
95.4279
ANGLE -80.2772 17.2227
12.1783
DIHED -13.0818 0.4289
0.3033
VDWAALS -26.9805 3.5347
2.4994
EEL -120.7679 3.7351
2.6411
1-4 VDW 0.1928 0.0016
0.0011
1-4 EEL 4.9305 0.0075
0.0053
EPB 131.0832 0.9076
0.6417
ENPOLAR -3.9183 0.0301
0.0213
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -1752.2148 117.0974
82.8004
DELTA G solv 127.1648 0.8774
0.6204
DELTA TOTAL -1625.0500 117.9748
83.4208
Pada tanggal Sab, 11 Apr 2020 pukul 19.00 David A Case <
david.case.rutgers.edu> menulis:
> On Sat, Apr 11, 2020, Nada Afiva wrote:
>
> >Yes I am using the single-trajectory approach.
>
> If you use the single-trajectory approach, then the bond energy
> contribution to binding should be zero. Try a very short simlation,
> even one frame: since you have saved the intermediate files, just do a
> single-step calculation (by hand) on receptor, ligand and complex, and
> do the delta calculations yourself. You may be able to see what is
> going wrong.
>
> ....dac
>
>
> _______________________________________________
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Received on Sat Apr 11 2020 - 23:30:01 PDT
