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
>
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Received on Mon Dec 05 2016 - 20:30:03 PST
