Dear Jason,
Many thanks fro the reply. The solvation energy shows positive values in PB
calculations as compared to GB ones. Below I just copied the results fro
both GB and PB calculations. Both calculation involves same system. Please
have a look.
*GB calculation*
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -4458.8179 34.8945
0.9870
EEL -39472.0783 118.8852
3.3626
EGB -6085.3517 95.2844
2.6951
ESURF 198.0542 2.8368
0.0802
G gas -43930.8962 118.3565
3.3476
G solv *-5887.2975* 94.5603
2.6746
TOTAL -49818.1937 66.1992
1.8724
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -2515.7191 28.2857
0.8000
EEL -22405.2101 93.6831
2.6498
EGB -3492.5229 74.4855
2.1068
ESURF 120.8083 2.1446
0.0607
G gas -24920.9292 91.5239
2.5887
G solv *-3371.7147* 73.8630
2.0892
TOTAL -28292.6438 52.9167
1.4967
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1805.9229 18.5645
0.5251
EEL -16332.3663 76.2526
2.1567
EGB -3402.4007 63.4785
1.7954
ESURF 97.6837 1.7862
0.0505
G gas -18138.2892 77.1853
2.1831
G solv *-3304.7170* 62.6905
1.7732
TOTAL -21443.0062 38.2786
1.0827
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -137.1759 7.7082
0.2180
EEL -734.5019 62.3795
1.7644
EGB 809.5720 59.2361
1.6755
ESURF -20.4378 0.9336
0.0264
DELTA G gas -871.6779 62.8862
1.7787
DELTA G solv *789.1342 * 58.7555
1.6619
DELTA TOTAL -82.5437 8.5046
0.2405
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
*PB calculation*
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -4453.0817 34.5145
4.3484
EEL -39464.0991 122.1391
15.3881
EPB -88.8720 15.7579
1.9853
ENPOLAR 126.1209 1.1655
0.1468
G gas -43917.1808 118.3991
14.9169
G solv *37.2490 * 15.9197
2.0057
TOTAL -43879.9318 114.0133
14.3643
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -2512.3457 27.6907
3.4887
EEL -22399.5909 97.4659
12.2795
EPB -57.9075 18.4141
2.3200
ENPOLAR 80.7826 0.8461
0.1066
G gas -24911.9366 92.5354
11.6584
G solv *22.8751 * 18.3217
2.3083
TOTAL -24889.0615 86.9242
10.9514
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1805.0607 19.7069
2.4828
EEL -16330.9144 85.1027
10.7219
EPB -105.9672 10.5846
1.3335
ENPOLAR 61.2667 0.9436
0.1189
G gas -18135.9751 85.9593
10.8298
G solv * -44.7004* 10.7940
1.3599
TOTAL -18180.6755 85.1325
10.7257
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -135.6753 6.0819
0.7662
EEL -733.5938 63.2610
7.9701
EPB 75.0027 20.2190
2.5474
ENPOLAR -15.9284 0.5842
0.0736
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -869.2691 63.3047
7.9756
DELTA G solv * 59.0743* 20.1582
2.5397
DELTA TOTAL -810.1948 72.0715
9.0802
-------------------------------------------------------------------------------
Many Thanks in Advance
Anu
On Wed, Dec 2, 2015 at 2:25 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Dec 2, 2015 at 8:59 AM, anu chandra <anu80125.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am working with a dimeric protein system and I am trying to calculate
> > the binding free energy change between two monomeric units in presence
> and
> > absence of bound ligand, using MMPBSA.py. Though the calculation finished
> > successfully, I find a huge difference between the GB and PB deltaG
> values
> > for the same system.
> >
> > In presnce of ligand, the GB value is -67.17 and the calculate PB value
> > for the same system is -675.37. Similarly, in absence of ligand, the GB
> > value is -82.54 and the calculate PB value for the same system is
> -810.19.
> >
>
> Something seems wrong with these numbers. GB and PB should be relatively
> close in general, and should certainly not differ by an order of
> magnitude...
>
> The GB results seem typical of MMPBSA results. PB does not.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Dec 02 2015 - 07:00:03 PST
