Re: [AMBER] Very low MMPBSA result

From: Ray Luo <rluo.uci.edu>
Date: Mon, 13 Apr 2020 13:21:22 -0700

It's very hard to guess out of blue what's going ... Please share with
us more information about your run, i.e. mmpbsa input file, command
line, and the Final_Results log file.

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 Mon, Apr 13, 2020 at 3:46 AM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> 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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Received on Mon Apr 13 2020 - 13:30:03 PDT
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