Dear Amber users,
I am calculation binding energy using MMPBSA.py on AMBER 12, I tried three
times and chose different number of frames of my trajectory. In the output
file I always get huge values for my VDW contribution. In my system I have
some attached glycans near to the binding site, but not directly in the
bonding site, I am taking them into calculations as well, but I don’t think
that may be the reason for huge VDW values since I have the similar out
values even in the absence of sugars.
I copied the out put file here. Will be very grateful if you guide me with
the possible solutions,
Best regards,
Maryam
| Run on Wed Jun 11 20:32:05 2014
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=100, verbose=1,
|# entropy=1,
|/
|&gb
| igb=2, saltcon=0.00
|/
|&pb
| istrng=0.00,
| inp=1,
| radiopt=0
|/
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Solvated complex topology file: all_solvate_MMPBSA.top
|Complex topology file: all_MMPBSA.top
|Receptor topology file: EGFR_MMPBSA.top
|Ligand topology file: EGF_MMPBSA.top
|Initial mdcrd(s): oligo_50_60ns_MMPBSA.mdcrd
|
|Receptor mask: ":1-614,662-715"
|Ligand mask: ":615-661"
|
|Calculations performed using 100 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 223805.6873 11244.1380
1124.4138
EEL -52842.0708 113.6366
11.3637
EGB -8301.1161 74.7854
7.4785
ESURF 279.0996 2.2720
0.2272
G gas 170963.6165 11240.7887
1124.0789
G solv -8022.0165 73.4541
7.3454
TOTAL 162941.6000 11240.5890
1124.0589
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 221705.4303 11231.2622
1123.1262
EEL -49485.4822 115.8710
11.5871
EGB -7766.3048 73.1855
7.3186
ESURF 271.4510 2.2494
0.2249
G gas 172219.9480 11221.9511
1122.1951
G solv -7494.8538 71.9711
7.1971
TOTAL 164725.0942 11225.7120
1122.5712
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 2234.3102 382.7137
38.2714
EEL -3140.3325 17.0751
1.7075
EGB -805.3784 15.6526
1.5653
ESURF 27.2004 0.3971
0.0397
G gas -906.0223 383.3543
38.3354
G solv -778.1781 15.4802
1.5480
TOTAL -1684.2004 383.3524
38.3352
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -134.0531 5.8754
0.5875
EEL -216.2561 25.2207
2.5221
EGB 270.5672 21.0542
2.1054
ESURF -19.5517 0.5051
0.0505
DELTA G gas -350.3093 25.7812
2.5781
DELTA G solv 251.0154 20.7866
2.0787
DELTA TOTAL -99.2938 7.9298
0.7930
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 223805.6873 11244.1380
1124.4138
EEL -52842.0708 113.6366
11.3637
EPB -8151.8725 78.6906
7.8691
ENPOLAR -41439.2677 238.3704
23.8370
G gas 170963.6165 11240.7887
1124.0789
G solv -49591.1402 286.2908
28.6291
TOTAL 121372.4763 11265.1054
1126.5105
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 221705.4303 11231.2622
1123.1262
EEL -49485.4822 115.8710
11.5871
EPB -7620.6988 74.7534
7.4753
ENPOLAR -40528.5458 241.3268
24.1327
G gas 172219.9480 11221.9511
1122.1951
G solv -48149.2447 286.2711
28.6271
TOTAL 124070.7034 11250.9119
1125.0912
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 2234.3102 382.7137
38.2714
EEL -3140.3325 17.0751
1.7075
EPB -780.7558 16.3540
1.6354
ENPOLAR -4136.6811 43.6240
4.3624
G gas -906.0223 383.3543
38.3354
G solv -4917.4369 50.4322
5.0432
TOTAL -5823.4592 388.4019
38.8402
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -134.0531 5.8754
0.5875
EEL -216.2561 25.2207
2.5221
EPB 249.5822 21.7402
2.1740
ENPOLAR 3225.9592 53.7083
5.3708
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -350.3093 25.7812
2.5781
DELTA G solv 3475.5414 60.5175
6.0517
DELTA TOTAL 3125.2321 55.0239
5.5024
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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Received on Thu Jun 12 2014 - 01:00:02 PDT
