Dear Amber experts,
I am writing this letter to seek help in some incorrect result found using
the “MMPBSA.py” and “MMPBSA.py.MPI” in Amber16 and Amber18.
Trial data from Amber Advanced Tutorial 3 was downloaded, from the
following links, for testing.
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section4.htm
However, results from the installed Amber16 and Amber18 were different from
the result provided in the tutorial.
The energy calculation in the Generalized Born model was correct, but the
result in the Poisson Boltzmann part was different.
Expected delta total should be ~-86.3579, but in all both non-MPI and MPI
MMPBSA.py I used in my machine, the result is ~-28.2058
Any clues on this solving this issue would help me a lot...
Thank you!
Best regards,
Marcus
Below is the input file and result files.
Input:
mmpbsa.in:
| Input file for running PB and GB
| &general
| endframe=50, verbose=1,
| # entropy=1,
| /
| &gb
| igb=2, saltcon=0.100
| /
| &pb
| istrng=0.100,
| /
Command:
| MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
prod*.mdcrd.gz > progress.log 2>&1
Result:
| Run on Tue Mar 24 18:18:22 2020
|
|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 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
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Thank you very much!
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Received on Thu Apr 02 2020 - 22:00:02 PDT
