Hi all!
Can anyone tell me why the values obtained from MMPBSA are so large? I also run mm_pbsa.pl and its results were plausible.
Thanks.
| Run on Sun Feb 5 02:59:59 EET 2012
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| startframe=1, endframe=50, interval=10,
| verbose=2, keep_files=2,
|/
|&gb
| igb=2, saltcon=0.150,
|/
|&pb
| istrng=0.15, fillratio=4.0
|/
|--------------------------------------------------------------
|Solvated complex topology file: com-wi.top
|Complex topology file: com.top
|Receptor topology file: rec.top
|Ligand topology file: lig.top
|Initial mdcrd(s): md6.mdcrd
|
|Best guess for receptor mask: ":1-180"
|Best guess for ligand mask: ":181"
|Ligand residue name is "L01"
|
|Calculations performed using 5 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE, AND/OR DIHED).
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
The most common cause of this is inconsistent charge definitions across topology files.
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 4468006.6134 2551485.0034 1275742.5017
ANGLE 192526.3776 114142.9719 57071.4859
DIHED 5676.9384 2569.8249 1284.9124
VDWAALS 6506271.2812 6537858.8705 3268929.4352
EEL -12778.8542 853.5929 426.7965
1-4 VDW 1596568.2907 911833.7055 455916.8527
1-4 EEL 7493.0783 1710.4797 855.2398
EGB -4769.3870 1653.1985 826.5993
ESURF 70.6792 2.8985 1.4493
G gas 12763763.7255 8616000.8089 4308000.4044
G solv -4698.7078 1652.4695 826.2348
TOTAL 12759065.0177 8615745.7068 4307872.8534
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 5024138.4848 3126481.3527 1563240.6764
ANGLE 178184.4100 103359.8225 51679.9112
DIHED 7187.4654 3082.1635 1541.0818
VDWAALS 1689047950663746.2500 2791321254216286.0000 1395660627108143.0000
EEL -9048.4383 3199.2678 1599.6339
1-4 VDW 7389795985768732.0000 12785878762283912.0000 6392939381141956.0000
1-4 EEL 4841.2467 3170.1210 1585.0605
EGB -4030.7533 968.7330 484.3665
ESURF 66.4631 4.6104 2.3052
G gas 9078843941637782.0000 15575901631105614.0000 7787950815552807.0000
G solv -3964.2901 972.5408 486.2704
TOTAL 9078843941633816.0000 15575901631105414.0000 7787950815552707.0000
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 1415003.3864 752781.9817 376390.9909
ANGLE 3330.1880 173.3357 86.6679
DIHED 187.2750 70.9806 35.4903
VDWAALS 8987259516.9542 15509991441.3610 7754995720.6805
EEL 134.7922 130.3638 65.1819
1-4 VDW 3716527.7997 6371013.7714 3185506.8857
1-4 EEL 16.5765 36.0347 18.0173
EGB -287.0035 130.2550 65.1275
ESURF 2.4828 0.2962 0.1481
G gas 8992394716.9719 15516634590.8691 7758317295.4346
G solv -284.5207 130.1194 65.0597
TOTAL 8992394432.4512 15516634540.8871 7758317270.4436
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -1971135.2578 1763041.8529 881520.9265
ANGLE 11011.7795 35153.8154 17576.9077
DIHED -1697.8020 1736.8869 868.4435
VDWAALS -1689056931416992.2500 2791336758363861.0000 1395668379181930.5000
EEL -3865.2081 2712.6319 1356.3160
1-4 VDW -7389795987888692.0000 12785878768538460.0000 6392939384269230.0000
1-4 EEL 2635.2552 3408.7393 1704.3696
EGB -451.6301 1651.3977 825.6988
ESURF 1.7332 4.6950 2.3475
DELTA G gas -9078852921268734.0000 15575917147905362.0000 7787958573952681.0000
DELTA G solv -449.8969 1650.1400 825.0700
DELTA G binding = -9078852921269184.0000 +/- 15575917147905742.0000 7787958573952871.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE, AND/OR DIHED).
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
The most common cause of this is inconsistent charge definitions across topology files.
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 4468006.6134 2551485.0034 1275742.5017
ANGLE 192526.3776 114142.9719 57071.4859
DIHED 5676.9384 2569.8249 1284.9124
VDWAALS 6506271.2812 6537858.8705 3268929.4352
EEL -12778.8542 853.5929 426.7965
1-4 VDW 1596568.2907 911833.7055 455916.8527
1-4 EEL 7493.0783 1710.4797 855.2398
EPB -3891.3737 1204.6692 602.3346
ECAVITY 58.0750 0.6146 0.3073
G gas 12763763.7255 8616000.8089 4308000.4044
G solv -3833.2987 1204.2659 602.1329
TOTAL 12759930.4268 8615928.5763 4307964.2881
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 5024138.4848 3126481.3527 1563240.6764
ANGLE 178184.4100 103359.8225 51679.9112
DIHED 7187.4654 3082.1635 1541.0818
VDWAALS 1689047950663554.5000 2791321254216004.5000 1395660627108002.2500
EEL -9048.4383 3199.2678 1599.6339
1-4 VDW 7389795985768732.0000 12785878762283912.0000 6392939381141956.0000
1-4 EEL 4841.2467 3170.1210 1585.0605
EPB -3163.4173 481.8471 240.9236
ECAVITY 58.6247 0.9822 0.4911
G gas 9078843941637590.0000 15575901631105336.0000 7787950815552668.0000
G solv -3104.7926 481.1980 240.5990
TOTAL 9078843941634484.0000 15575901631105264.0000 7787950815552632.0000
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 1415003.3864 752781.9817 376390.9909
ANGLE 3330.1880 173.3357 86.6679
DIHED 187.2750 70.9806 35.4903
VDWAALS 8987259516.9542 15509991441.3610 7754995720.6805
EEL 134.7922 130.3638 65.1819
1-4 VDW 3716527.7997 6371013.7714 3185506.8857
1-4 EEL 16.5765 36.0347 18.0173
EPB -266.8480 125.3258 62.6629
ECAVITY 2.9364 0.4849 0.2424
G gas 8992394716.9719 15516634590.8691 7758317295.4346
G solv -263.9116 124.9746 62.4873
TOTAL 8992394453.0603 15516634540.5456 7758317270.2728
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -1971135.2578 1763041.8529 881520.9265
ANGLE 11011.7795 35153.8154 17576.9077
DIHED -1697.8020 1736.8869 868.4435
VDWAALS -1689056931416800.5000 2791336758363579.5000 1395668379181789.7500
EEL -3865.2081 2712.6319 1356.3160
1-4 VDW -7389795987888692.0000 12785878768538460.0000 6392939384269230.0000
1-4 EEL 2635.2552 3408.7393 1704.3696
EPB -461.1084 1149.5946 574.7973
ECAVITY -3.4861 1.0773 0.5387
DELTA G gas -9078852921268544.0000 15575917147905082.0000 7787958573952541.0000
DELTA G solv -464.5945 1150.1092 575.0546
DELTA G binding = -9078852921269008.0000 +/- 15575917147905610.0000 7787958573952805.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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Received on Sat Feb 04 2012 - 17:30:02 PST
