Tried again with basic generic parameters. The PB results are
still bizarre.
I'm getting the same values on 2 different machines using 2 different OS's
Files are attached.
| Run on Thu Dec 20 13:46:36 2012
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| interval=10,
| verbose=1,
|# entropy=1,
|/
|&gb
| saltcon=0.100
|/
|&pb
| istrng=0.100, inp=1, radiopt=0
|/
|&alanine_scanning
|/
|--------------------------------------------------------------
|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
|Mutant complex topology file: complex103.prmtop
|Mutant receptor topology file: ../protein.prmtop
|Mutant ligand topology file: peptide103.prmtop
|Initial mdcrd(s): prod1.mdcrd.gz
|
|Receptor mask: ":1-87"
|Ligand mask: ":88-106"
|
|Calculations performed using 50 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 -682.0769 18.1879
2.5722
EEL -7105.7544 89.2399
12.6204
EGB -1761.1677 86.3443
12.2109
ESURF 53.3449 2.1585
0.3053
G gas -7787.8313 96.7750
13.6861
G solv -1707.8227 84.8790
12.0037
TOTAL -9495.6540 29.2096
4.1309
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -533.1672 13.2827
1.8785
EEL -5893.7948 63.9261
9.0405
EGB -1484.4252 64.3861
9.1056
ESURF 47.8004 1.2265
0.1734
G gas -6426.9620 65.9628
9.3285
G solv -1436.6247 63.5284
8.9843
TOTAL -7863.5867 21.2503
3.0052
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -51.4980 4.9814
0.7045
EEL -1112.7783 32.3386
4.5734
EGB -431.0815 28.6901
4.0574
ESURF 17.2915 0.2743
0.0388
G gas -1164.2764 31.9185
4.5140
G solv -413.7901 28.5145
4.0326
TOTAL -1578.0664 10.4672
1.4803
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -97.4117 14.5839
2.0625
EEL -99.1813 28.4013
4.0166
EGB 154.3390 31.8477
4.5039
ESURF -11.7470 1.7622
0.2492
DELTA G gas -196.5929 38.2549
5.4101
DELTA G solv 142.5921 30.4919
4.3122
DELTA TOTAL -54.0009 9.8976
1.3997
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
K103A MUTANT:
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -676.7151 17.8731
2.5276
EEL -6952.8738 78.5670
11.1111
EGB -1849.4765 75.0327
10.6112
ESURF 53.7723 2.0673
0.2924
G gas -7629.5889 83.9892
11.8779
G solv -1795.7042 73.8494
10.4439
TOTAL -9425.2932 28.2685
3.9978
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -533.1672 13.2827
1.8785
EEL -5893.7948 63.9261
9.0405
EGB -1484.4252 64.3861
9.1056
ESURF 47.8004 1.2265
0.1734
G gas -6426.9620 65.9628
9.3285
G solv -1436.6247 63.5284
8.9843
TOTAL -7863.5867 21.2503
3.0052
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -50.2227 4.8232
0.6821
EEL -1016.8797 17.7425
2.5092
EGB -457.0862 14.1321
1.9986
ESURF 17.2581 0.2073
0.0293
G gas -1067.1023 17.7434
2.5093
G solv -439.8281 14.0642
1.9890
TOTAL -1506.9304 10.0612
1.4229
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -93.3253 14.0196
1.9827
EEL -42.1993 27.3134
3.8627
EGB 92.0348 27.6026
3.9036
ESURF -11.2862 1.7042
0.2410
DELTA G gas -135.5246 33.3161
4.7116
DELTA G solv 80.7486 26.7078
3.7771
DELTA TOTAL -54.7760 9.4931
1.3425
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
RESULT OF ALANINE SCANNING: (K103A) DELTA DELTA G binding = 0.7751 +/-
1.6145
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -682.0769 18.1879
2.5722
EEL -7105.7544 89.2399
12.6204
EPB -1843.3860 84.3276
11.9257
ENPOLAR -7895.3567 338.1798
47.8258
G gas -7787.8313 96.7750
13.6861
G solv -9738.7428 394.3993
55.7765
TOTAL -17526.5741 327.0635
46.2538
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -533.1672 13.2827
1.8785
EEL -5893.7948 63.9261
9.0405
EPB -1542.5632 63.4845
8.9781
ENPOLAR -7113.1093 149.7471
21.1774
G gas -6426.9620 65.9628
9.3285
G solv -8655.6724 200.2324
28.3171
TOTAL -15082.6345 155.0666
21.9297
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -51.4980 4.9814
0.7045
EEL -1112.7783 32.3386
4.5734
EPB -441.3410 28.3329
4.0069
ENPOLAR -2792.9997 46.4237
6.5653
G gas -1164.2764 31.9185
4.5140
G solv -3234.3407 63.5687
8.9900
TOTAL -4398.6171 45.0261
6.3677
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -97.4117 14.5839
2.0625
EEL -99.1813 28.4013
4.0166
EPB 140.5181 31.4729
4.4509
ENPOLAR 2010.7523 295.3602
41.7702
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -196.5929 38.2549
5.4101
DELTA G solv 2151.2704 317.7442
44.9358
DELTA TOTAL 1954.6774 287.7796
40.6982
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
K103A MUTANT:
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -676.7151 17.8731
2.5276
EEL -6952.8738 78.5670
11.1111
EPB -1926.0225 73.7476
10.4295
ENPOLAR -7897.2824 325.3416
46.0103
G gas -7629.5889 83.9892
11.8779
G solv -9823.3049 366.5358
51.8360
TOTAL -17452.8938 315.8032
44.6613
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -533.1672 13.2827
1.8785
EEL -5893.7948 63.9261
9.0405
EPB -1542.5632 63.4845
8.9781
ENPOLAR -7113.1093 149.7471
21.1774
G gas -6426.9620 65.9628
9.3285
G solv -8655.6724 200.2324
28.3171
TOTAL -15082.6345 155.0666
21.9297
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -50.2227 4.8232
0.6821
EEL -1016.8797 17.7425
2.5092
EPB -463.7980 13.1878
1.8650
ENPOLAR -2704.9421 40.8040
5.7706
G gas -1067.1023 17.7434
2.5093
G solv -3168.7402 46.8262
6.6222
TOTAL -4235.8425 40.0329
5.6615
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -93.3253 14.0196
1.9827
EEL -42.1993 27.3134
3.8627
EPB 80.3387 27.9239
3.9490
ENPOLAR 1920.7690 283.2766
40.0614
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -135.5246 33.3161
4.7116
DELTA G solv 2001.1077 296.5305
41.9357
DELTA TOTAL 1865.5831 275.8093
39.0053
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
RESULT OF ALANINE SCANNING: (K103A) DELTA DELTA G binding = 89.0943 +/-
22.5695
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
On Wed, Dec 19, 2012 at 11:20 AM, Jonathan Gough <jonathan.d.gough.gmail.com
> wrote:
> 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 Thu Dec 20 2012 - 11:30:03 PST
