Nadaafiva,
My guess is that your receptor and ligand are bonded. You can't define
them as separate molecules if they are bonded.
All the best,
Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sat, Apr 11, 2020 at 11:11 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> 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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> >
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Received on Sun Apr 12 2020 - 09:30:02 PDT