Hello Ray,
Sorry for the delayed reply. I just noticed that I have used wrong
coordinates that messed up the whole calculation. Please excuse me for this
Many thanks once again
Anu
On Thu, Dec 3, 2015 at 6:26 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Hi Anu,
>
> How about you email me, OFF THE LIST, all the MMPBSA files, i.e.
> input, prmtop, mdcrd files etc. Please email files for the complex
> only with three snapshots.
>
> 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 Thu, Dec 3, 2015 at 2:28 AM, anu chandra <anu80125.gmail.com> wrote:
> > 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
> >> >> _______________________________________________
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> >> >>
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Received on Sat Dec 05 2015 - 04:00:04 PST
