Hello Ray,
Thanks for the reply. I am using AmberTools 15 and version 14.0 of
MMPBSA.py for the calculation.
--------------------------------------------------------------------------------
|*MMPBSA.py Version=14.0*
|Complex topology file: COMPLEX.top
|Receptor topology file: RECEPTOR.top
|Ligand topology file: LIGAND.top
|Initial mdcrd(s): md1.nc
|
|Receptor mask: ":1-294,527-545"
|Ligand mask: ":295-526"
|
|Calculations performed using 63 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Many thanks
Anu
On Thu, Dec 3, 2015 at 12:09 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Looks like your protein/complex EPB's are very small. Which version
> are you using for these runs?
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Wed, Dec 2, 2015 at 6:48 AM, anu chandra <anu80125.gmail.com> wrote:
> > 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 Thu Dec 03 2015 - 02:30:03 PST
