Custom Search
-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Mon, Dec 5, 2016 at 8:15 PM, Hai Nguyen <nhai.qn.gmail.com> wrote: > hi > > I don't see anything wrong either. You can try with igb=8 too (recommend to > use mbondi2 for GBSA in this case). > > Hai > > On Mon, Dec 5, 2016 at 11:10 PM, Aronica, Pietro < > pietro.aronica07.imperial.ac.uk> wrote: > >> Hello, >> >> I have recently run a simulation of a simple protein receptor + peptide >> ligand system and tried to calculate the MMGBSA and MMPBSA difference in >> energy between the bound and unbound state. >> >> In my experience, the absolute value for the PB tends to be a few kcal/mol >> lower than the GB one, but in this system this was not the case. While the >> GB was -67.7195 ± 5.4461, the PB was -54.7742 ± 11.3891. This is not an >> isolated result and the same pattern repeats across different runs. The >> discrepancy and the much higher error of the PB give me pause and I have >> been looking at the system to determine if something was wrong or if I made >> a mistake. >> >> As far as I can tell I have used all the input files correctly, or at >> least in the same way I usually do. What can I be on the lookout for? What >> should I check in order to determine the cause of this bizarre result? >> Should I even be worried? >> >> I also print the entire GB and PB output files, in case these are of any >> help. >> >> If there are suggestions or comments, please do let me know. >> >> Cheers >> >> Pietro Aronica >> >> >> GB: >> >> | Run on Tue Dec 6 00:03:58 2016 >> | >> |Input file: >> |-------------------------------------------------------------- >> |&general >> |/ >> |&gb >> | igb=5, surften=0.0050 >> |/ >> |&decomp >> | idecomp=2, dec_verbose=1 >> |/ >> |-------------------------------------------------------------- >> |MMPBSA.py Version=14.0 >> |Solvated complex topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_mbondi.prmtop >> |Complex topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_com_mbondi2.prmtop >> |Receptor topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_rec_mbondi2.prmtop >> |Ligand topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_lig_mbondi2.prmtop >> |Initial mdcrd(s): ../Total_run.mdcrd >> | >> |Receptor mask: ":1-517" >> |Ligand mask: ":518-520" >> | >> |Calculations performed using 100 complex frames. >> | >> |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 -4461.2579 33.9886 >> 3.3989 >> EEL -39522.6040 144.1058 >> 14.4106 >> EGB -6004.7227 119.4563 >> 11.9456 >> ESURF 99.6832 2.0092 >> 0.2009 >> >> G gas -43983.8620 147.5266 >> 14.7527 >> G solv -5905.0395 118.7491 >> 11.8749 >> >> TOTAL -49888.9015 69.0225 >> 6.9023 >> >> >> Receptor: >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -4403.5819 33.5620 >> 3.3562 >> EEL -38747.6831 144.3997 >> 14.4400 >> EGB -6221.3471 120.6745 >> 12.0674 >> ESURF 103.4116 1.9760 >> 0.1976 >> >> G gas -43151.2651 147.2434 >> 14.7243 >> G solv -6117.9355 120.0168 >> 12.0017 >> >> TOTAL -49269.2005 68.8915 >> 6.8892 >> >> >> Ligand: >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -6.5483 1.2008 >> 0.1201 >> EEL -258.8440 13.4295 >> 1.3430 >> EGB -288.8132 12.4559 >> 1.2456 >> ESURF 2.2239 0.0509 >> 0.0051 >> >> G gas -265.3922 12.9580 >> 1.2958 >> G solv -286.5893 12.4173 >> 1.2417 >> >> TOTAL -551.9815 3.7165 >> 0.3717 >> >> >> Differences (Complex - Receptor - Ligand): >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -51.1277 4.2314 >> 0.4231 >> EEL -516.0770 17.5053 >> 1.7505 >> EGB 505.4375 15.2402 >> 1.5240 >> ESURF -5.9523 0.1398 >> 0.0140 >> >> DELTA G gas -567.2047 16.5366 >> 1.6537 >> DELTA G solv 499.4852 15.2016 >> 1.5202 >> >> DELTA TOTAL -67.7195 5.4461 >> 0.5446 >> >> >> >> PB: >> >> | Run on Tue Dec 6 08:33:43 2016 >> | >> |Input file: >> |-------------------------------------------------------------- >> |&general >> |/ >> |&pb >> | inp=1, radiopt=0, cavity_surften=0.0072 >> |/ >> |&decomp >> | idecomp=2, dec_verbose=1 >> |/ >> |-------------------------------------------------------------- >> |MMPBSA.py Version=14.0 >> |Solvated complex topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_mbondi.prmtop >> |Complex topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_com_mbondi.prmtop >> |Receptor topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_rec_mbondi.prmtop >> |Ligand topology file: /home/pietroa/Charge_ >> derivation/GLU/MMPBSA/FF99SB_KEK_lig_mbondi.prmtop >> |Initial mdcrd(s): ../Total_run.mdcrd >> | >> |Receptor mask: ":1-517" >> |Ligand mask: ":518-520" >> | >> |Calculations performed using 100 complex frames. >> |Poisson Boltzmann calculations performed using internal PBSA solver in >> sander. >> | >> |All units are reported in kcal/mole. >> ------------------------------------------------------------ >> ------------------- >> ------------------------------------------------------------ >> ------------------- >> >> POISSON BOLTZMANN: >> >> Complex: >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -4461.2579 33.9886 >> 3.3989 >> EEL -39522.6040 144.1058 >> 14.4106 >> EPB -5966.1358 119.2844 >> 11.9284 >> ENPOLAR 156.8866 1.7105 >> 0.1710 >> >> G gas -43983.8620 147.5266 >> 14.7527 >> G solv -5809.2492 118.3545 >> 11.8354 >> >> TOTAL -49793.1112 75.5242 >> 7.5524 >> >> >> Receptor: >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -4403.5819 33.5620 >> 3.3562 >> EEL -38747.6831 144.3997 >> 14.4400 >> EPB -6196.9759 123.0006 >> 12.3001 >> ENPOLAR 158.8439 1.7092 >> 0.1709 >> >> G gas -43151.2651 147.2434 >> 14.7243 >> G solv -6038.1320 122.1447 >> 12.2145 >> TOTAL -49189.3971 72.9118 >> 7.2912 >> >> >> Ligand: >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -6.5483 1.2008 >> 0.1201 >> EEL -258.8440 13.4295 >> 1.3430 >> EPB -288.9018 12.0239 >> 1.2024 >> ENPOLAR 5.3541 0.0626 >> 0.0063 >> >> G gas -265.3922 12.9580 >> 1.2958 >> G solv -283.5477 11.9841 >> 1.1984 >> >> TOTAL -548.9399 3.7137 >> 0.3714 >> >> >> Differences (Complex - Receptor - Ligand): >> Energy Component Average Std. Dev. Std. Err. of >> Mean >> ------------------------------------------------------------ >> ------------------- >> VDWAALS -51.1277 4.2314 >> 0.4231 >> EEL -516.0770 17.5053 >> 1.7505 >> EPB 519.7418 15.9509 >> 1.5951 >> ENPOLAR -7.3113 0.1295 >> 0.0129 >> EDISPER 0.0000 0.0000 >> 0.0000 >> >> DELTA G gas -567.2047 16.5366 >> 1.6537 >> DELTA G solv 512.4305 15.9443 >> 1.5944 >> >> DELTA TOTAL -54.7742 11.3891 >> 1.1389 >> >> _______________________________________________ >> 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 Tue Dec 06 2016 - 18:30:02 PST