Hello,
I am trying to replicated AMBER MMPBSA tutorial:
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
which with amber16 installation resulted in differences between outputs.
The last lines (POISSON BOLTZMANN part) in tutorial are:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -56.2934 2.9265 0.4139
EEL -38.0300 3.2114 0.4542
EPB 57.6402 3.0642 0.4333
ECAVITY -5.0423 0.1683 0.0238
DELTA G gas -94.3234 18.8778 2.6697
DELTA G solv 52.5978 3.0688 0.4340
DELTA G binding = -41.7256 +/- 2.9618 0.4189
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
But my result is:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956
0.4095
EEL -38.0301 3.1822
0.4500
EPB 56.7520 3.5086
0.4962
ENPOLAR -43.4196 1.2202
0.1726
EDISPER 74.2997 1.3514
0.1911
DELTA G gas -94.3222 3.3476
0.4734
DELTA G solv 87.6321 3.8310
0.5418
DELTA TOTAL -6.6901 3.8563
0.5454
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Maybe, someone can explain these differences?
Thank you in advance!
The complete output below:
| Run on Tue Jan 23 07:35:13 2018
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| endframe=50, keep_files=2,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: 1err.solvated.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): 1err_prod.mdcrd
|
|Receptor mask: ":1-240"
|Ligand mask: ":241"
|Ligand residue name is "RAL"
|
|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 -2013.3861 20.1108
2.8441
EEL -16938.6434 84.8707
12.0025
EGB -3506.9860 67.1003
9.4894
ESURF 97.4744 1.3170
0.1863
G gas -18952.0295 81.3542
11.5052
G solv -3409.5116 66.5951
9.4180
TOTAL -22361.5411 36.3100
5.1350
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529
2.6945
EEL -16895.0333 84.6812
11.9757
EGB -3528.7058 67.6664
9.5695
ESURF 101.2621 1.2926
0.1828
G gas -18850.2679 80.7202
11.4156
G solv -3427.4437 67.2065
9.5044
TOTAL -22277.7116 34.9512
4.9428
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320
0.2874
EEL -5.5800 2.0133
0.2847
EGB -28.4852 0.5979
0.0846
ESURF 4.4805 0.0425
0.0060
G gas -7.4395 3.0299
0.4285
G solv -24.0047 0.6040
0.0854
TOTAL -31.4442 3.2513
0.4598
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956
0.4095
EEL -38.0301 3.1822
0.4500
EGB 50.2050 2.5622
0.3624
ESURF -8.2682 0.2700
0.0382
DELTA G gas -94.3222 3.3476
0.4734
DELTA G solv 41.9369 2.4569
0.3475
DELTA TOTAL -52.3853 2.4400
0.3451
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -2013.3861 20.1108
2.8441
EEL -16938.6434 84.8707
12.0025
EPB -3243.8422 65.3230
9.2381
ENPOLAR 1965.5188 6.3800
0.9023
EDISPER -1107.5209 6.8746
0.9722
G gas -18952.0295 81.3542
11.5052
G solv -2385.8443 64.1413
9.0709
TOTAL -21337.8739 41.6822
5.8948
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529
2.6945
EEL -16895.0333 84.6812
11.9757
EPB -3269.8301 65.8433
9.3116
ENPOLAR 1956.8205 6.3089
0.8922
EDISPER -1131.1692 6.4443
0.9114
G gas -18850.2679 80.7202
11.4156
G solv -2444.1788 64.7272
9.1538
TOTAL -21294.4467 40.4322
5.7180
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320
0.2874
EEL -5.5800 2.0133
0.2847
EPB -30.7641 0.6756
0.0955
ENPOLAR 52.1180 0.2043
0.0289
EDISPER -50.6514 0.3305
0.0467
G gas -7.4395 3.0299
0.4285
G solv -29.2976 0.7438
0.1052
TOTAL -36.7370 3.0716
0.4344
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956
0.4095
EEL -38.0301 3.1822
0.4500
EPB 56.7520 3.5086
0.4962
ENPOLAR -43.4196 1.2202
0.1726
EDISPER 74.2997 1.3514
0.1911
DELTA G gas -94.3222 3.3476
0.4734
DELTA G solv 87.6321 3.8310
0.5418
DELTA TOTAL -6.6901 3.8563
0.5454
--
pagarbiai, Audrius Laurynėnas
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Received on Tue Jan 23 2018 - 04:30:02 PST
