You are not setting the surface tension coefficients for the nonpolar
solvation energy. The default values were for inp=2. If you look at
the EPB and EGB, they are qualitatively consistent.
Ray
On Thu, Dec 20, 2012 at 10:58 AM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> 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 - 11:30:05 PST
