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--- VDWAALS -1863.7981 16.9946 2.4034 EEL -17200.7406 75.1582 10.6290 EPB -3190.9098 65.7247 9.2949 ENPOLAR 90.4931 1.0269 0.1452 G gas -19064.5387 73.4400 10.3860 G solv -3100.4167 65.6183 9.2798 TOTAL -22164.9555 42.9677 6.0765 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ---------------------------------------------------------------------------- --- VDWAALS -1268.1869 14.0928 1.9930 EEL -11557.0789 71.0248 10.0444 EPB -2471.4166 55.7345 7.8820 ENPOLAR 62.9686 0.6248 0.0884 G gas -12825.2658 66.1471 9.3546 G solv -2408.4480 55.5642 7.8580 TOTAL -15233.7138 34.6337 4.8979 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ---------------------------------------------------------------------------- --- VDWAALS -529.3073 9.3319 1.3197 EEL -4684.4887 35.7985 5.0627 EPB -1664.1943 27.4311 3.8793 ENPOLAR 37.5578 0.5324 0.0753 G gas -5213.7960 37.0299 5.2368 G solv -1626.6365 27.2864 3.8589 TOTAL -6840.4326 25.4836 3.6039 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ---------------------------------------------------------------------------- --- VDWAALS -66.3039 4.2329 0.5986 EEL -959.1730 34.5550 4.8868 EPB 944.7011 33.8872 4.7924 ENPOLAR -10.0333 0.3947 0.0558 EDISPER 0.0000 0.0000 0.0000 DELTA G gas -1025.4769 34.3707 4.8607 DELTA G solv 934.6678 33.8259 4.7837 DELTA TOTAL -90.8091 7.8144 1.1051 ---------------------------------------------------------------------------- --- ---------------------------------------------------------------------------- --- Re: [AMBER] Differences on MMPBSA calculation results To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEk9e3p7rP_yhLuZ+XvWQBTOJo92j+Ry1HCFiRSXR5DXJ+jMjg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 I just sent an answer to what was, in effect, the exact same question just a minute ago. The reason MMPBSA.py gives different PB values is a different nonpolar solvation free energy model. Try putting inp=1 in the &pb section and rerun the calculations. Agreement with tutorial results should be much better. HTH, Jason On Mon, Oct 19, 2015 at 10:58 AM, MarcZhang <progress0935zhang.gmail.com> wrote: > Dear Amber user group > > > > I found differences on my MMPBSA calculation results, when I tried to > reproduce the results in the Amber tutorial. > > > > The binding free energy of Ras-Raf was calculated using the exact input > files and trajectory files from the tutorial. (AMBER ADVANCED TUTORIALS > TUTORIAL 3 - SECTION 3.1) > > > > The calculation results suggested that MMGBSA returned decent values but > results of MMPBSA were far deviated from the values given in the tutorial. > > > > The only differences I found in the results file is that my calculation > used > mmpbsa_py_energy PBSA solver instead of sander in tutorial. > > > > Is this the reason for the deviations? How can I change the solver, if it > is > cause. > > > > Thank you very much for your help! > > > > Cheers > > > > > > Here is the my calculation results: > > | Run on Mon Oct 19 14:16:21 2015 > > | > > |Input file: > > |-------------------------------------------------------------- > > |Input file for running PB and GB > > |&general > > | endframe=50, verbose=1, > > |# entropy=1, > > |/ > > |&gb > > | igb=2, saltcon=0.100 > > |/ > > |&pb > > | istrng=0.100, > > |/ > > |-------------------------------------------------------------- > > |MMPBSA.py Version=13.0 > > |Solvated complex topology file: ras-raf_solvated.prmtop > > |Complex topology file: ras-raf.prmtop > > |Receptor topology file: ras.prmtop > > |Ligand topology file: raf.prmtop > > |Initial mdcrd(s): prod.mdcrd > > | > > |Receptor mask: ":1-166" > > |Ligand mask: ":167-242" > > | > > |Calculations performed using 50 complex frames. > > |Poisson Boltzmann calculations performed using internal PBSA solver in > mmpbsa_py_energy > > | > > |Generalized Born ESURF calculated using 'LCPO' surface areas > > | > > |All units are reported in kcal/mole. > > > ---------------------------------------------------------------------------- > --- > > > ---------------------------------------------------------------------------- > --- > > > > GENERALIZED BORN: > > > > Complex: > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -1863.7981 16.9946 > 2.4034 > > EEL -17200.7406 75.1582 > 10.6290 > > EGB -3249.6527 64.5827 > 9.1334 > > ESURF 91.3567 1.3775 > 0.1948 > > > > G gas -19064.5387 73.4400 > 10.3860 > > G solv -3158.2960 64.1112 > 9.0667 > > > > TOTAL -22222.8347 39.9219 > 5.6458 > > > > > > Receptor: > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -1268.1869 14.0928 > 1.9930 > > EEL -11557.0789 71.0248 > 10.0444 > > EGB -2532.0576 57.1271 > 8.0790 > > ESURF 64.2856 1.1041 > 0.1561 > > > > G gas -12825.2658 66.1471 > 9.3546 > > G solv -2467.7721 56.9614 > 8.0556 > > > > TOTAL -15293.0379 32.1381 > 4.5450 > > > > > > Ligand: > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -529.3073 9.3319 > 1.3197 > > EEL -4684.4887 35.7985 > 5.0627 > > EGB -1688.9704 26.2775 > 3.7162 > > ESURF 37.0477 0.6113 > 0.0865 > > > > G gas -5213.7960 37.0299 > 5.2368 > > G solv -1651.9227 26.1219 > 3.6942 > > > > TOTAL -6865.7187 22.1937 > 3.1387 > > > > > > Differences (Complex - Receptor - Ligand): > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -66.3039 4.2329 > 0.5986 > > EEL -959.1730 34.5550 > 4.8868 > > EGB 971.3753 32.7146 > 4.6265 > > ESURF -9.9766 0.3725 > 0.0527 > > > > DELTA G gas -1025.4769 34.3707 > 4.8607 > > DELTA G solv 961.3987 32.5152 > 4.5983 > > > > DELTA TOTAL -64.0781 6.3096 > 0.8923 > > > > > > > ---------------------------------------------------------------------------- > --- > > > ---------------------------------------------------------------------------- > --- > > > > POISSON BOLTZMANN: > > > > Complex: > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -1863.7981 16.9946 > 2.4034 > > EEL -17200.7406 75.1582 > 10.6290 > > EPB -3190.9098 65.7247 > 9.2949 > > ENPOLAR 1933.4589 6.8742 > 0.9722 > > EDISPER -1134.8693 6.9333 > 0.9805 > > > > G gas -19064.5387 73.4400 > 10.3860 > > G solv -2392.3202 64.9746 > 9.1888 > > > > TOTAL -21456.8589 44.3294 > 6.2691 > > > > > > Receptor: > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -1268.1869 14.0928 > 1.9930 > > EEL -11557.0789 71.0248 > 10.0444 > > EPB -2471.4166 55.7345 > 7.8820 > > ENPOLAR 1323.4880 5.2717 > 0.7455 > > EDISPER -791.2302 4.6135 > 0.6525 > > > > G gas -12825.2658 66.1471 > 9.3546 > > G solv -1939.1588 54.5734 > 7.7178 > > > > TOTAL -14764.4246 36.1469 > 5.1119 > > > > > > Ligand: > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -529.3073 9.3319 > 1.3197 > > EEL -4684.4887 35.7985 > 5.0627 > > EPB -1664.1943 27.4311 > 3.8793 > > ENPOLAR 660.9497 3.2883 > 0.4650 > > EDISPER -445.7195 3.9547 > 0.5593 > > > > G gas -5213.7960 37.0299 > 5.2368 > > G solv -1448.9641 27.7526 > 3.9248 > > > > TOTAL -6662.7601 26.7643 > 3.7850 > > > > > > Differences (Complex - Receptor - Ligand): > > Energy Component Average Std. Dev. Std. Err. of > Mean > > > ---------------------------------------------------------------------------- > --- > > VDWAALS -66.3039 4.2329 > 0.5986 > > EEL -959.1730 34.5550 > 4.8868 > > EPB 944.7011 33.8872 > 4.7924 > > ENPOLAR -50.9787 1.8037 > 0.2551 > > EDISPER 102.0803 2.6804 > 0.3791 > > > > DELTA G gas -1025.4769 34.3707 > 4.8607 > > DELTA G solv 995.8027 33.8122 > 4.7818 > > > > DELTA TOTAL -29.6742 7.9567 > 1.1252 > > > > > > > ---------------------------------------------------------------------------- > --- > > > ---------------------------------------------------------------------------- > --- > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Oct 20 2015 - 03:30:03 PDT