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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Thu, Jul 6, 2017 at 2:49 AM, NADIA RAHMAH <nadiiarah.apps.ipb.ac.id> wrote: > Sorry to send not complete results. I didnt tell you this is PB Delta G. PB > Delta total value is positive while GB Delta is negaive, Is it problem or > something error? > > |Input file: > |-------------------------------------------------------------- > |Sample input file for GB and PB calculation > |&general > |startframe=1, endframe=10000, interval=50, > |verbose=2, keep_files=0, > |/ > |&gb > |igb=5, saltcon=0.150, > |/ > |&pb > |istrng=0.15, fillratio=4.0 > |/ > |-------------------------------------------------------------- > |MMPBSA.py Version=14.0 > |Complex topology file: complexnobox_3wi7rbb.prmtop > |Receptor topology file: protein.prmtop > |Ligand topology file: ligan.prmtop > |Initial mdcrd(s): 3wi7rbb.nc > | > |Receptor mask: ":1-291" > |Ligand mask: ":292" > |Ligand residue name is "UNL" > | > |Calculations performed using 200 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 > ------------------------------------------------------------------------------- > BOND 912.5936 23.3491 > 1.6510 > ANGLE 2428.7787 34.2154 > 2.4194 > DIHED 3769.6586 21.4600 > 1.5175 > VDWAALS -2466.7203 22.2716 > 1.5748 > EEL -19829.1418 106.3164 > 7.5177 > 1-4 VDW 1084.1896 14.5553 > 1.0292 > 1-4 EEL 9856.0973 41.1595 > 2.9104 > EGB -2557.6201 85.2699 > 6.0295 > ESURF 89.0527 1.7420 > 0.1232 > > G gas -4244.5444 103.4226 > 7.3131 > G solv -2468.5674 84.5367 > 5.9776 > > TOTAL -6713.1118 51.4808 > 3.6402 > > > Receptor: > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND 911.3783 23.2978 > 1.6474 > ANGLE 2422.5641 34.0504 > 2.4077 > DIHED 3768.2360 21.4450 > 1.5164 > VDWAALS -2448.4510 22.0682 > 1.5605 > EEL -19821.6598 106.3786 > 7.5221 > 1-4 VDW 1083.3272 14.6062 > 1.0328 > 1-4 EEL 9857.1039 41.1947 > 2.9129 > EGB -2565.1932 85.3334 > 6.0340 > ESURF 89.9441 1.7262 > 0.1221 > > G gas -4227.5013 104.0079 > 7.3545 > G solv -2475.2491 84.5944 > 5.9817 > > TOTAL -6702.7503 51.5860 > 3.6477 > > Ligand: > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND 1.2152 0.9774 > 0.0691 > ANGLE 6.2146 2.0044 > 0.1417 > DIHED 1.4225 0.6671 > 0.0472 > VDWAALS -0.0078 0.3911 > 0.0277 > EEL -0.4298 0.2128 > 0.0150 > 1-4 VDW 0.8625 0.4192 > 0.0296 > 1-4 EEL -1.0066 0.2333 > 0.0165 > EGB -2.4506 0.0873 > 0.0062 > ESURF 1.6260 0.0096 > 0.0007 > > G gas 8.2706 2.4641 > 0.1742 > G solv -0.8245 0.0865 > 0.0061 > > TOTAL 7.4461 2.4730 > 0.1749 > > > Differences (Complex - Receptor - Ligand): > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND -0.0000 0.0001 > 0.0000 > ANGLE 0.0000 0.0001 > 0.0000 > DIHED 0.0000 0.0000 > 0.0000 > VDWAALS -18.2614 1.2729 > 0.0900 > EEL -7.0523 1.8874 > 0.1335 > 1-4 VDW -0.0000 0.0001 > 0.0000 > 1-4 EEL -0.0000 0.0000 > 0.0000 > EGB 10.0237 1.5415 > 0.1090 > ESURF -2.5175 0.0801 > 0.0057 > > DELTA G gas -25.3137 2.2277 > 0.1575 > DELTA G solv 7.5062 1.5431 > 0.1091 > > DELTA TOTAL -17.8075 1.8112 > 0.1281 > > > ------------------------------------------------------------------------------- > ------------------------------------------------------------------------------- > > POISSON BOLTZMANN: > > Complex: > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND 912.5936 23.3491 > 1.6510 > ANGLE 2428.7787 34.2154 > 2.4194 > DIHED 3769.6586 21.4600 > 1.5175 > VDWAALS -2466.7203 22.2716 > 1.5748 > EEL -19829.1418 106.3164 > 7.5177 > 1-4 VDW 1084.1896 14.5553 > 1.0292 > 1-4 EEL 9856.0973 41.1595 > 2.9104 > EPB -2639.8863 86.9608 > 6.1491 > ENPOLAR 2191.4591 8.4002 > 0.5940 > EDISPER -1130.7876 9.7908 > 0.6923 > > G gas -4244.5444 103.4226 > 7.3131 > G solv -1579.2148 86.0073 > 6.0816 > > TOTAL -5823.7592 56.4697 > 3.9930 > > > Receptor: > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND 911.3783 23.2978 > 1.6474 > ANGLE 2422.5641 34.0504 > 2.4077 > DIHED 3768.2360 21.4450 > 1.5164 > VDWAALS -2448.4510 22.0682 > 1.5605 > EEL -19821.6598 106.3786 > 7.5221 > 1-4 VDW 1083.3272 14.6062 > 1.0328 > 1-4 EEL 9857.1039 41.1947 > 2.9129 > EPB -2660.8632 86.9206 > 6.1462 > ENPOLAR 2190.4601 8.3759 > 0.5923 > EDISPER -1139.5953 9.7842 > 0.6919 > > G gas -4227.5013 104.0079 > 7.3545 > G solv -1609.9985 85.9000 > 6.0740 > > TOTAL -5837.4998 55.4874 > 3.9235 > > Ligand: > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND 1.2152 0.9774 > 0.0691 > ANGLE 6.2146 2.0044 > 0.1417 > DIHED 1.4225 0.6671 > 0.0472 > VDWAALS -0.0078 0.3911 > 0.0277 > EEL -0.4298 0.2128 > 0.0150 > 1-4 VDW 0.8625 0.4192 > 0.0296 > 1-4 EEL -1.0066 0.2333 > 0.0165 > EPB -2.2980 0.0776 > 0.0055 > ENPOLAR 14.9804 0.1359 > 0.0096 > EDISPER -13.3213 0.0859 > 0.0061 > > G gas 8.2706 2.4641 > 0.1742 > G solv -0.6389 0.1582 > 0.0112 > > TOTAL 7.6317 2.4782 > 0.1752 > > > Differences (Complex - Receptor - Ligand): > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > BOND -0.0000 0.0001 > 0.0000 > ANGLE 0.0000 0.0001 > 0.0000 > DIHED 0.0000 0.0000 > 0.0000 > VDWAALS -18.2614 1.2729 > 0.0900 > EEL -7.0523 1.8874 > 0.1335 > 1-4 VDW -0.0000 0.0001 > 0.0000 > 1-4 EEL -0.0000 0.0000 > 0.0000 > EPB 23.2749 5.0209 > 0.3550 > ENPOLAR -13.9814 0.2315 > 0.0164 > EDISPER 22.1291 0.5543 > 0.0392 > > DELTA G gas -25.3137 2.2277 > 0.1575 > DELTA G solv 31.4226 5.0797 > 0.3592 > > DELTA TOTAL 6.1089 4.1135 > 0.2909 > > > > > > > On Thu, Jul 6, 2017 at 4:27 PM, Elvis Martis <elvis.martis.bcp.edu.in> > wrote: > >> HI, >> I assume this delta G is the results of either PB or GB calculations. >> In the absence of entropy calculations, this delta G total reflects only >> the enthalpy component and hence not the true delta G binding. >> >> Best Regards >> Elvis Martis >> Mumbai, INDIA. >> >> ________________________________________ >> From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id> >> Sent: 06 July 2017 12:45:40 >> To: AMBER Mailing List >> Subject: [AMBER] MMPBSA Delta total results >> >> Hello Amber Users, I want to ask about MMPBSA results, at the end of the >> results, I get DELTA TOTAL : >> >> DELTA G gas -24.9391 2.2411 >> 0.1585 >> DELTA G solv 34.0352 3.5423 >> 0.2505 >> >> DELTA TOTAL 9.0961 3.7742 >> 0.2669 >> >> I want to ask, is DELTA TOTAL same with Delta G Binding? because I dont >> find Delta G Binding in my results. and the delta total value is so >> positive. Thanks >> -- >> >> *Regards,* >> *Nadia Rahmah* >> *Department of Physics Undergraduate Student - 2013Bogor Agricultural >> University* >> _______________________________________________ >> 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 >> > > > > -- > > *Regards,* > *Nadia Rahmah* > *Department of Physics Undergraduate Student - 2013Bogor Agricultural > University* > _______________________________________________ > 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 Jul 06 2017 - 19:30:03 PDT