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-- 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 >> >> _______________________________________________ >> >> AMBER mailing list >> >> AMBER.ambermd.org >> >> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> > _______________________________________________ >> > AMBER mailing list >> > AMBER.ambermd.org >> > http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Dec 03 2015 - 10:30:05 PST