Dear Prof Luo,
After inspecting all the pdb files during MD, there was no covalent bond
between receptor and ligand was detected.
I hope any suggestion regarding this matter.
Thank you.
best regards,
nadaafiva
Pada tanggal Min, 12 Apr 2020 pukul 23.02 Ray Luo <rluo.uci.edu> menulis:
> 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 Mon Apr 13 2020 - 04:00:02 PDT
