Hi,I got a high vdw valve ,while proceed alanine scanning.anybody can help
me?
mmpbsa.in:
sample input file for running alanine scanning
&general
startframe=1661, endframe=3360, verbose=1,interval=3
/
&gb
igb=2, saltcon=0.100,
/
&alanine_scanning
/
outputs:
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -4664.8348 40.3305
1.6937
EEL -40112.9182 173.0475
7.2673
EGB -7018.5738 153.4492
6.4443
ESURF 203.3883 5.7364
0.2409
G gas -44777.7531 185.3851
7.7854
G solv -6815.1854 149.3497
6.2721
TOTAL -51592.9385 70.5856
2.9643
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -3852.8181 35.9492
1.5097
EEL -33869.6229 139.0234
5.8384
EGB -6083.8337 122.0876
5.1272
ESURF 188.3695 4.8630
0.2042
G gas -37722.4410 143.5441
6.0283
G solv -5895.4642 119.7273
5.0281
TOTAL -43617.9051 59.2586
2.4886
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -628.5072 11.6704
0.4901
EEL -5893.5004 48.8451
2.0513
EGB -1368.1701 37.6007
1.5791
ESURF 41.7911 0.9258
0.0389
G gas -6522.0076 48.8561
2.0518
G solv -1326.3790 37.2698
1.5652
TOTAL -7848.3866 26.0491
1.0940
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -183.5096 9.0852
0.3815
EEL -349.7949 73.0042
3.0659
EGB 433.4300 62.2139
2.6127
ESURF -26.7722 1.1122
0.0467
DELTA G gas -533.3045 76.2163
3.2008
DELTA G solv 406.6578 61.3718
2.5774
DELTA TOTAL -126.6467 17.8443
0.7494
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
M97A MUTANT:
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -751.7663 55398.8392
2326.5326
EEL -40115.8693 173.6839
7.2940
EGB -7020.4082 153.8018
6.4591
ESURF 203.8655 5.7235
0.2404
G gas -40867.6356 55398.0821
2326.5008
G solv -6816.5427 149.7153
6.2875
TOTAL -47684.1783 55402.7368
2326.6962
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -3848.7059 35.9760
1.5109
EEL -33873.9839 139.1567
5.8440
EGB -6083.5749 122.3434
5.1379
ESURF 187.9564 4.8560
0.2039
G gas -37722.6898 143.8340
6.0405
G solv -5895.6185 119.9551
5.0376
TOTAL -43618.3083 59.2558
2.4885
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -628.5072 11.6704
0.4901
EEL -5893.5004 48.8451
2.0513
EGB -1368.1701 37.6007
1.5791
ESURF 41.7911 0.9258
0.0389
G gas -6522.0076 48.8561
2.0518
G solv -1326.3790 37.2698
1.5652
TOTAL -7848.3866 26.0491
1.0940
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 3725.4469 55399.7456
2326.5706
EEL -348.3851 72.6127
3.0494
EGB 431.3368 61.6242
2.5880
ESURF -25.8820 1.0969
0.0461
DELTA G gas 3377.0618 55397.2666
2326.4665
DELTA G solv 405.4548 60.7919
2.5530
DELTA TOTAL 3782.5166 55399.9116
2326.5776
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
RESULT OF ALANINE SCANNING: (M97A) DELTA DELTA G binding = -3909.1633 +/-
55400.2945
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Received on Thu May 08 2014 - 05:00:03 PDT
