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From: Ray Luo <rluo.uci.edu>

Date: Wed, 7 Dec 2016 10:01:32 -0800

The NP portion is really small for the final delta G from MMPB/GBSA,

so either parameter is okay, I think ... unless you use inp=2 in

MMPBSA.

All the best,

Ray

Date: Wed, 7 Dec 2016 10:01:32 -0800

The NP portion is really small for the final delta G from MMPB/GBSA,

so either parameter is okay, I think ... unless you use inp=2 in

MMPBSA.

All the best,

Ray

-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Dec 6, 2016 at 6:14 PM, Aronica, Pietro <pietro.aronica07.imperial.ac.uk> wrote: > Yes, I am not using the same surface tension for both because I am following the recommendations of the manual for GB5 and PB4 respectively (page 699). Should I used different flavours of MMPBSA/MMGBSA? These settings seem to work for all other systems, it is just this one that has given me a peculiar result with PB specifically. > > ________________________________ > From: Ray Luo <rluo.uci.edu> > Sent: 06 December 2016 17:03:46 > To: AMBER Mailing List > Subject: Re: [AMBER] MMGBSA vs MMPBSA > > Pietro, > > For the NP part, you are not using the same coefficient ... 5 > cal/mol-A^2 for GB and 7.3 cal/mol-A^2 for PB. > > The delta G EPB and EGB are 519 kcal/mol and 505 kcal/mol, > respectively. They are different but apparently close. > > All the best, > Ray > -- > 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/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Dec 07 2016 - 10:30:02 PST

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