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-- 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 > > > > > > > > > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Apr 13 2020 - 13:30:03 PDT