[AMBER] MMGBSA vs MMPBSA

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Tue, 6 Dec 2016 04:10:48 +0000

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
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