Custom Search
-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Mon, Apr 24, 2023 at 4:02 AM devendra.prajapat.cys19--- via AMBER <amber.ambermd.org> wrote: > > Dear Amber Users, > > I tried to reproduce the MMPBSA results using the MMPBSA tutorial > (https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm__;!!CzAuKJ42GuquVTTmVmPViYEvSg!P4EbBS1dvxLX0FqzE1O41uTzDK-0eLPqDRZMua8DIMwMi3kHiPpUcKyYs7rBgz_WnTX7TQI1DLo$ ). > I downloaded all the required topology and coordinate files from the > tutorial itself. > When I compared my results (-28.2 kcal/mol) with the ones given in the > tutorial (-86.35 kcal/mol), I found that they drastically differ for > MMPBSA values. However, MMGBSA values are reproducible. The origin of > such a difference is DELTA G solv values. > > I am using amber18, and the only difference is that I used MMPBSA.py.MPI > instead of serial version (MMPBSA.py). > > I am not getting, where I am going wrong. > > Many thanks > Sincerely > Devendra > > Below is the output data: > **************************************************************************************************************** > Run on Mon Apr 24 15:52:42 2023 > | > |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=14.0 > |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 50.0 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 -3042.9732 69.0328 > 9.7627 > ENPOLAR 1933.4589 6.8742 > 0.9722 > EDISPER -1130.8283 6.9218 > 0.9789 > > G gas -19064.5387 73.4400 > 10.3860 > G solv -2240.3425 68.3262 > 9.6628 > > TOTAL -21304.8812 47.8829 > 6.7717 > > > 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 -2441.2908 57.8922 > 8.1872 > ENPOLAR 1323.4880 5.2717 > 0.7455 > EDISPER -787.7775 4.5944 > 0.6497 > > G gas -12825.2658 66.1471 > 9.3546 > G solv -1905.5803 56.8799 > 8.0440 > > TOTAL -14730.8461 40.8423 > 5.7760 > > > 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 -1548.7938 27.2871 > 3.8590 > ENPOLAR 660.9497 3.2883 > 0.4650 > EDISPER -444.1892 3.9350 > 0.5565 > > G gas -5213.7960 37.0299 > 5.2368 > G solv -1332.0333 27.6670 > 3.9127 > > TOTAL -6545.8293 29.0059 > 4.1021 > > > 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 947.1114 33.4524 > 4.7309 > ENPOLAR -50.9787 1.8037 > 0.2551 > EDISPER 101.1385 2.6639 > 0.3767 > > DELTA G gas -1025.4769 34.3707 > 4.8607 > DELTA G solv 997.2711 33.4305 > 4.7278 > > DELTA TOTAL -28.2058 8.1968 > 1.1592 > > *************************************************************************************************************** > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!P4EbBS1dvxLX0FqzE1O41uTzDK-0eLPqDRZMua8DIMwMi3kHiPpUcKyYs7rBgz_WnTX7zQ0Yxq4$ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Apr 24 2023 - 10:30:02 PDT