Dear Amber Users,
I tried to reproduce the MMPBSA results using the MMPBSA tutorial
(
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm).
I downloaded all the required topology and coordinate files from the
tutorial itself.
When I compared my results (-28.2 kcal/mol) with the ones given in the
tutorial (-86.35 kcal/mol), I found that they drastically differ for
MMPBSA values. However, MMGBSA values are reproducible. The origin of
such a difference is DELTA G solv values.
I am using amber18, and the only difference is that I used MMPBSA.py.MPI
instead of serial version (MMPBSA.py).
I am not getting, where I am going wrong.
Many thanks
Sincerely
Devendra
Below is the output data:
****************************************************************************************************************
Run on Mon Apr 24 15:52:42 2023
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=50, verbose=1,
|# entropy=1,
|/
|&gb
| igb=2, saltcon=0.100
|/
|&pb
| istrng=0.100,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: ras-raf_solvated.prmtop
|Complex topology file: ras-raf.prmtop
|Receptor topology file: ras.prmtop
|Ligand topology file: raf.prmtop
|Initial mdcrd(s): prod.mdcrd
|
|Receptor mask: ":1-166"
|Ligand mask: ":167-242"
|
|Calculations performed using 50.0 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -1863.7981 16.9946
2.4034
EEL -17200.7406 75.1582
10.6290
EGB -3249.6527 64.5827
9.1334
ESURF 91.3567 1.3775
0.1948
G gas -19064.5387 73.4400
10.3860
G solv -3158.2960 64.1112
9.0667
TOTAL -22222.8347 39.9219
5.6458
Receptor:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -1268.1869 14.0928
1.9930
EEL -11557.0789 71.0248
10.0444
EGB -2532.0576 57.1271
8.0790
ESURF 64.2856 1.1041
0.1561
G gas -12825.2658 66.1471
9.3546
G solv -2467.7721 56.9614
8.0556
TOTAL -15293.0379 32.1381
4.5450
Ligand:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -529.3073 9.3319
1.3197
EEL -4684.4887 35.7985
5.0627
EGB -1688.9704 26.2775
3.7162
ESURF 37.0477 0.6113
0.0865
G gas -5213.7960 37.0299
5.2368
G solv -1651.9227 26.1219
3.6942
TOTAL -6865.7187 22.1937
3.1387
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -66.3039 4.2329
0.5986
EEL -959.1730 34.5550
4.8868
EGB 971.3753 32.7146
4.6265
ESURF -9.9766 0.3725
0.0527
DELTA G gas -1025.4769 34.3707
4.8607
DELTA G solv 961.3987 32.5152
4.5983
DELTA TOTAL -64.0781 6.3096
0.8923
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -1863.7981 16.9946
2.4034
EEL -17200.7406 75.1582
10.6290
EPB -3042.9732 69.0328
9.7627
ENPOLAR 1933.4589 6.8742
0.9722
EDISPER -1130.8283 6.9218
0.9789
G gas -19064.5387 73.4400
10.3860
G solv -2240.3425 68.3262
9.6628
TOTAL -21304.8812 47.8829
6.7717
Receptor:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -1268.1869 14.0928
1.9930
EEL -11557.0789 71.0248
10.0444
EPB -2441.2908 57.8922
8.1872
ENPOLAR 1323.4880 5.2717
0.7455
EDISPER -787.7775 4.5944
0.6497
G gas -12825.2658 66.1471
9.3546
G solv -1905.5803 56.8799
8.0440
TOTAL -14730.8461 40.8423
5.7760
Ligand:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -529.3073 9.3319
1.3197
EEL -4684.4887 35.7985
5.0627
EPB -1548.7938 27.2871
3.8590
ENPOLAR 660.9497 3.2883
0.4650
EDISPER -444.1892 3.9350
0.5565
G gas -5213.7960 37.0299
5.2368
G solv -1332.0333 27.6670
3.9127
TOTAL -6545.8293 29.0059
4.1021
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -66.3039 4.2329
0.5986
EEL -959.1730 34.5550
4.8868
EPB 947.1114 33.4524
4.7309
ENPOLAR -50.9787 1.8037
0.2551
EDISPER 101.1385 2.6639
0.3767
DELTA G gas -1025.4769 34.3707
4.8607
DELTA G solv 997.2711 33.4305
4.7278
DELTA TOTAL -28.2058 8.1968
1.1592
***************************************************************************************************************
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Received on Mon Apr 24 2023 - 04:30:02 PDT
