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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 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/amberReceived on Wed Dec 02 2015 - 16:30:03 PST