Dear Amber Users,
I am trying to calculate the free energy of a
protein-peptide system using mmpbsa.py script from Amber12.
My input script file for the purpose is the following.
sample input file for MM-GBSA calculation and DECOMPOSITION
&general
startframe=1, endframe=50000, interval=10,
verbose=2, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&decomp
idecomp=2,
dec_verbose=0,
csv_format=0,
/
The calculation goes on fine. The final statistics is as follows.
|MMPBSA.py Version=12.0
|Complex topology file: ../../complex.parmtop
|Receptor topology file: ../../protein.parmtop
|Ligand topology file: ../../peptide.parmtop
|Initial mdcrd(s):
../../../centering/prod_cen_strip_sol_ion.mdcrd
|
|Receptor mask: ":1-189"
|Ligand mask: ":190-203"
|
|Calculations performed using 5000 complex frames.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 647.4911 21.6041 0.3055
ANGLE 1682.8402 31.8009 0.4497
DIHED 2132.8508 18.9976 0.2687
VDWAALS 4539.8345 1530.7455 21.6480
EEL -13699.1924 108.8936 1.5400
1-4 VDW 752.4023 11.6313 0.1645
1-4 EEL 7589.7396 52.8488 0.7474
EGB -3163.9703 88.1210 1.2462
ESURF 84.4256 1.7838 0.0252
G gas 3645.9662 1532.2705 21.6696
G solv -3079.5447 87.5957 1.2388
TOTAL 566.4215 1530.7715 21.6484
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 599.0144 20.8510 0.2949
ANGLE 1564.8283 30.4181 0.4302
DIHED 1985.2735 18.0507 0.2553
VDWAALS -1475.0583 18.4672 0.2612
EEL -12804.7448 99.3452 1.4050
1-4 VDW 694.2489 11.2516 0.1591
1-4 EEL 7385.6220 52.5821 0.7436
EGB -3188.6682 89.0650 1.2596
ESURF 79.9245 1.4009 0.0198
G gas -2050.8160 103.4176 1.4625
G solv -3108.7437 88.4805 1.2513
TOTAL -5159.5597 42.0311 0.5944
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 48.4767 5.9530 0.0842
ANGLE 118.0119 8.4970 0.1202
DIHED 147.5773 5.1734 0.0732
VDWAALS 6069.3243 1530.2449 21.6409
EEL -373.5075 16.7907 0.2375
1-4 VDW 58.1534 3.0488 0.0431
1-4 EEL 204.1176 10.3060 0.1457
EGB -506.2401 12.3892 0.1752
ESURF 14.2383 0.4659 0.0066
G gas 6272.1537 1530.1827 21.6401
G solv -492.0018 12.4146 0.1756
TOTAL 5780.1519 1530.2265 21.6407
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0000 0.0000
ANGLE -0.0000 0.0000 0.0000
DIHED -0.0000 0.0000 0.0000
VDWAALS -54.4314 5.9129 0.0836
EEL -520.9400 67.0862 0.9487
1-4 VDW 0.0000 0.0000 0.0000
1-4 EEL -0.0000 0.0001 0.0000
EGB 530.9380 61.6686 0.8721
ESURF -9.7372 0.8343 0.0118
DELTA G gas -575.3715 67.4110 0.9533
DELTA G solv 521.2008 61.2946 0.8668
DELTA TOTAL -54.1707 8.7948 0.1244
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
The "DELTA TOTAL" value for the complex and ligand doesn't look
correct to me. The energy values are positive and the standard
deviations are huge. The same values for the Receptors and finally for
the Differences (Complex - Receptor - Ligand) looks fine.
Is there anything wrong with the calculation or is there something I
am missing??
Will be glad if someone can kindly help me out with this.
Thank you,
Dilraj.
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Received on Mon May 13 2013 - 04:00:02 PDT
