I ran a MMPBSA computation and the data isn't exactly what I expected. I
am wondering if and what I am missing. Do these results make sense?
protein - peptide MD was done in explicit solvent, 1 Na atom was used for
charge balance.
the total G is negative for the GB, but the PB is positive.
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| interval=10,
| verbose=1,
|# entropy=1,
|/
|&gb
| igb=2, saltcon=0.10
|/
|&pb
| istrng=0.000, inp=1, radiopt=0
|/
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Solvated complex topology file: eq9-tip3.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: protein.prmtop
|Ligand topology file: peptide.prmtop
|Initial mdcrd(s): prod10.mdcrd.gz
| prod1.mdcrd.gz
| prod2.mdcrd.gz
| prod3.mdcrd.gz
| prod4.mdcrd.gz
| prod5.mdcrd.gz
| prod6.mdcrd.gz
| prod7.mdcrd.gz
| prod8.mdcrd.gz
| prod9.mdcrd.gz
|
|Receptor mask: ":1-87"
|Ligand mask: ":88-106"
|
|Calculations performed using 500 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -689.3528 20.3887
0.9118
EEL -7209.9961 101.0713
4.5200
EGB -1780.7197 95.8827
4.2880
ESURF 51.4798 2.2001
0.0984
G gas -7899.3488 106.4936
4.7625
G solv -1729.2399 94.4497
4.2239
TOTAL -9628.5887 32.2263
1.4412
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -538.6278 13.0420
0.5833
EEL -5947.4782 77.6774
3.4738
EGB -1529.2047 67.3836
3.0135
ESURF 46.7337 1.1744
0.0525
G gas -6486.1060 79.4018
3.5510
G solv -1482.4710 66.6187
2.9793
TOTAL -7968.5770 29.5391
1.3210
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -53.1702 4.4720
0.2000
EEL -1071.2554 35.6834
1.5958
EGB -484.7833 29.3741
1.3136
ESURF 17.6407 0.3696
0.0165
G gas -1124.4256 35.4379
1.5848
G solv -467.1426 29.1083
1.3018
TOTAL -1591.5682 12.9770
0.5803
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -97.5548 14.2769
0.6385
EEL -191.2625 72.3842
3.2371
EGB 233.2682 69.9734
3.1293
ESURF -12.8945 1.9697
0.0881
DELTA G gas -288.8172 79.1380
3.5392
DELTA G solv 220.3737 68.5420
3.0653
DELTA TOTAL -68.4435 13.1973
0.5902
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -689.3528 20.3887
0.9118
EEL -7209.9961 101.0713
4.5200
EPB -1733.3105 92.7881
4.1496
ENPOLAR -7646.4575 330.6507
14.7871
G gas -7899.3488 106.4936
4.7625
G solv -9379.7680 389.7384
17.4296
TOTAL -17279.1168 324.8458
14.5275
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -538.6278 13.0420
0.5833
EEL -5947.4782 77.6774
3.4738
EPB -1490.9879 65.4619
2.9275
ENPOLAR -6960.8637 146.4187
6.5480
G gas -6486.1060 79.4018
3.5510
G solv -8451.8517 192.4196
8.6053
TOTAL -14937.9577 141.5962
6.3324
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -53.1702 4.4720
0.2000
EEL -1071.2554 35.6834
1.5958
EPB -470.2825 28.6124
1.2796
ENPOLAR -2836.5168 53.5764
2.3960
G gas -1124.4256 35.4379
1.5848
G solv -3306.7993 74.0624
3.3122
TOTAL -4431.2249 49.5550
2.2162
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -97.5548 14.2769
0.6385
EEL -191.2625 72.3842
3.2371
EPB 227.9599 68.7656
3.0753
ENPOLAR 2150.9231 302.5804
13.5318
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -288.8172 79.1380
3.5392
DELTA G solv 2378.8830 351.2831
15.7099
DELTA TOTAL 2090.0658 293.9258
13.1448
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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Received on Wed Dec 19 2012 - 08:30:03 PST
