Re: [AMBER] controversy in PBSA and GBSA results

From: Ray Luo <rluo.uci.edu> Date: Mon, 5 Oct 2020 07:39:59 -0700

--
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 Sun, Oct 4, 2020 at 10:29 PM <h_sahakyan.mb.sci.am> wrote:
>
> Ray, This is the GB/PB energy outputs, =============================ProteinA-ProteinB============================= GENERALIZED BORN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 2725.3297 41.0831 6.4958 ANGLE 7367.8541 54.2788 8.5822 DIHED 11207.6796 43.9051 6.9420 VDWAALS -7274.1573 46.0537 7.2817 EEL -61408.6416 202.0172 31.9417 1-4 VDW 3169.0364 22.1976 3.5098 1-4 EEL 32795.9798 100.4060 15.8756 EGB -10312.8531 176.3519 27.8837 ESURF 249.9682 4.6790 0.7398 G gas -11416.9193 218.5464 34.5552 G solv -10062.8849 173.7562 27.4733 TOTAL -21479.8042 103.5699 16.3758 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1342.0930 31.3887 4.9630 ANGLE 3567.1121 45.9150 7.2598 DIHED 5619.1685 30.9328 4.8909 VDWAALS -3549.7595 34.2059 5.4084 EEL -29912.8128 121.7239 19.2462 1-4 VDW 1566.19!
>  35 14.1202 2.2326 1-4 EEL 15892.4384 56.0425 8.8611 EGB -5507.2758 102.4422 16.1975 ESURF 137.7332 2.7734 0.4385 G gas -5475.5668 130.5967 20.6491 G solv -5369.5425 101.5974 16.0640 TOTAL -10845.1094 76.5534 12.1042 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1383.2367 30.9529 4.8941 ANGLE 3800.7420 38.5974 6.1028 DIHED 5588.5111 28.3730 4.4862 VDWAALS -3577.3224 30.9141 4.8879 EEL -31153.2314 144.5584 22.8567 1-4 VDW 1602.8429 16.7684 2.6513 1-4 EEL 16903.5414 66.8804 10.5747 EGB -5214.6007 111.5863 17.6433 ESURF 132.7417 3.0813 0.4872 G gas -5451.6797 136.6881 21.6123 G solv -5081.8590 110.1224 17.4119 TOTAL -10533.5387 60.0692 9.4978 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 0.0000 0.0000 0.0000 ANGLE -0.0000 0.0000 0.0000 DIHED -0.00!
>  00 0.0000 0.0000 VDWAALS -147.0755 7.2141 1.1407 EEL -342.5974 69.4194 10.9762 1-4 VDW 0.0000 0.0000 0.0000 1-4 EEL 0.0000 0.0000 0.0000 EGB 409.0234 68.9800 10.9067 ESURF -20.5068 0.8173 0.1292 DELTA G gas -489.6728 69.5677 10.9996 DELTA G solv 388.5166 68.7186 10.8654 DELTA TOTAL -101.1562 8.0872 1.2787 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- POISSON BOLTZMANN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 2725.3297 41.0831 6.4958 ANGLE 7367.8541 54.2788 8.5822 DIHED 11207.6796 43.9051 6.9420 VDWAALS -7274.1573 46.0537 7.2817 EEL -61408.6416 202.0172 31.9417 1-4 VDW 3169.0364 22.1976 3.5098 1-4 EEL 32795.9798 100.4060 15.8756 EPB -10174.9865 175.5525 27.7573 ENPOLAR 165.4609 2.0068 0.3173 G gas -11416.9193 218.5464 34.5552 G solv -10009.5256 174.3982 27.5748 TOTAL -21426.4449 105.1211 16.6211 Receptor: Energy Component Avera!
>  ge Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1342.0930 31.3887 4.9630 ANGLE 3567.1121 45.9150 7.2598 DIHED 5619.1685 30.9328 4.8909 VDWAALS -3549.7595 34.2059 5.4084 EEL -29912.8128 121.7239 19.2462 1-4 VDW 1566.1935 14.1202 2.2326 1-4 EEL 15892.4384 56.0425 8.8611 EPB -5441.3221 102.1315 16.1484 ENPOLAR 91.9854 1.3461 0.2128 G gas -5475.5668 130.5967 20.6491 G solv -5349.3367 101.5115 16.0504 TOTAL -10824.9035 81.0513 12.8153 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1383.2367 30.9529 4.8941 ANGLE 3800.7420 38.5974 6.1028 DIHED 5588.5111 28.3730 4.4862 VDWAALS -3577.3224 30.9141 4.8879 EEL -31153.2314 144.5584 22.8567 1-4 VDW 1602.8429 16.7684 2.6513 1-4 EEL 16903.5414 66.8804 10.5747 EPB -5145.9284 108.7467 17.1944 ENPOLAR 90.0991 1.3797 0.2182 G gas -5451.6797 136.6881 21.6123 G solv -5055.8293 108.!
>  0809 17.0891 TOTAL -10507.5090 64.1981 10.1506 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 0.0000 0.0000 0.0000 ANGLE -0.0000 0.0000 0.0000 DIHED -0.0000 0.0000 0.0000 VDWAALS -147.0755 7.2141 1.1407 EEL -342.5974 69.4194 10.9762 1-4 VDW 0.0000 0.0000 0.0000 1-4 EEL 0.0000 0.0000 0.0000 EPB 412.2640 67.1989 10.6251 ENPOLAR -16.6236 0.6017 0.0951 EDISPER 0.0000 0.0000 0.0000 DELTA G gas -489.6728 69.5677 10.9996 DELTA G solv 395.6404 67.1314 10.6144 DELTA TOTAL -94.0324 11.0928 1.7539 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- =============================ProteinA-LIG-ProteinB============================= GENERALIZED BORN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 2737.3322 41.3055 6.5310 ANG!
>  LE 7333.8369 71.8044 11.3533 DIHED 11218.1209 38.0561 6.0172 VDWAALS -7422.8674 45.3559 7.1714 EEL -54650.8088 338.0472 53.4500 1-4 VDW 3190.0712 23.5033 3.7162 1-4 EEL 32080.1560 92.7789 14.6696 EGB -16551.3691 306.1813 48.4115 ESURF 237.4909 3.9943 0.6316 G gas -5514.1591 353.8185 55.9436 G solv -16313.8781 304.4377 48.1358 TOTAL -21828.0372 97.3040 15.3851 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1363.7120 26.3447 4.1655 ANGLE 3578.4560 50.0156 7.9082 DIHED 5636.0660 25.5571 4.0409 VDWAALS -3668.3318 23.5124 3.7176 EEL -27505.4650 276.6625 43.7442 1-4 VDW 1588.0136 14.5250 2.2966 1-4 EEL 15529.9179 56.4484 8.9253 EGB -7668.3472 247.7521 39.1730 ESURF 127.9532 2.2695 0.3588 G gas -3477.6312 274.6726 43.4295 G solv -7540.3939 247.5025 39.1336 TOTAL -11018.0252 66.9695 10.5888 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean --------------------------------!
>  ----------------------------------------------- BOND 1373.6202 30.7634 4.8641 ANGLE 3755.3809 49.0162 7.7501 DIHED 5582.0549 27.8715 4.4069 VDWAALS -3603.9974 39.3143 6.2161 EEL -28701.4676 134.8711 21.3250 1-4 VDW 1602.0576 17.8692 2.8254 1-4 EEL 16550.2381 61.8584 9.7807 EGB -7374.0285 101.8508 16.1040 ESURF 130.8560 2.5404 0.4017 G gas -3442.1134 134.9075 21.3307 G solv -7243.1725 100.5387 15.8966 TOTAL -10685.2858 73.8118 11.6707 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 0.0000 0.0000 0.0000 ANGLE 0.0000 0.0000 0.0000 DIHED 0.0000 0.0001 0.0000 VDWAALS -150.5382 6.0288 0.9532 EEL 1556.1238 75.6932 11.9681 1-4 VDW -0.0000 0.0001 0.0000 1-4 EEL -0.0000 0.0000 0.0000 EGB -1508.9934 71.3682 11.2843 ESURF -21.3183 0.7796 0.1233 DELTA G gas 1405.5855 75.0676 11.8692 DELTA G solv -1530.3117 71.1930 11.2566 DELTA TOTAL -124.7262 8.6285 1.3643 ---------------------------------------------------------------------!
>  ---------- ------------------------------------------------------------------------------- POISSON BOLTZMANN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 2737.3322 41.3055 6.5310 ANGLE 7333.8369 71.8044 11.3533 DIHED 11218.1209 38.0561 6.0172 VDWAALS -7422.8674 45.3559 7.1714 EEL -54650.8088 338.0472 53.4500 1-4 VDW 3190.0712 23.5033 3.7162 1-4 EEL 32080.1560 92.7789 14.6696 EPB -16346.1727 305.9787 48.3795 ENPOLAR 161.7247 1.6960 0.2682 G gas -5514.1591 353.8185 55.9436 G solv -16184.4479 305.1032 48.2411 TOTAL -21698.6070 98.7523 15.6141 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1363.7120 26.3447 4.1655 ANGLE 3578.4560 50.0156 7.9082 DIHED 5636.0660 25.5571 4.0409 VDWAALS -3668.3318 23.5124 3.7176 EEL -27505.4650 276.6625 43.7442 1-4 VDW 1588.0136 14.5250 2.2966 1-4 !
>  EEL 15529.9179 56.4484 8.9253 EPB -7578.4422 248.7017 39.3232 ENPOLAR 88.4054 0.9022 0.1426 G gas -3477.6312 274.6726 43.4295 G solv -7490.0368 248.4030 39.2760 TOTAL -10967.6680 68.3699 10.8102 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 1373.6202 30.7634 4.8641 ANGLE 3755.3809 49.0162 7.7501 DIHED 5582.0549 27.8715 4.4069 VDWAALS -3603.9974 39.3143 6.2161 EEL -28701.4676 134.8711 21.3250 1-4 VDW 1602.0576 17.8692 2.8254 1-4 EEL 16550.2381 61.8584 9.7807 EPB -7318.4354 98.1016 15.5112 ENPOLAR 89.3015 1.0541 0.1667 G gas -3442.1134 134.9075 21.3307 G solv -7229.1339 97.6060 15.4329 TOTAL -10671.2472 76.1852 12.0459 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- BOND 0.0000 0.0000 0.0000 ANGLE 0.0000 0.0000 0.0000 DIHED 0.0000 0.0001 0.0000 VDWAALS -150.5382 6.0288 0.9532 EEL 1556.1238 75.6932 11.9681 1-4 VDW -0.0000 !
>  0.0001 0.0000 1-4 EEL -0.0000 0.0000 0.0000 EPB -1449.2951 71.7408 11.3432 ENPOLAR -15.9821 0.4283 0.0677 EDISPER 0.0000 0.0000 0.0000 DELTA G gas 1405.5855 75.0676 11.8692 DELTA G solv -1465.2772 71.6115 11.3228 DELTA TOTAL -59.6917 15.8837 2.5114 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Kind regards, Harutyun
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