Dear Amber Users,
I ran MMGBSA analysis with ptraj for two different states of a
protein.In one state the receptor protein is glycosylated with nine
oligosaccharides and in one it is not. The problem is for glycosylated
system the out put file contains a huge number for VDW forces.The output
file of both systems are below.Did I do something wrong while running
the analysis?
Thank you for your help.
Maryam
The non-gly system:
Complex:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -5005.1864 33.5955 3.3595
EEL -47343.5689 69.8255 6.9825
EGB -6976.5858 43.5705 4.3570
ESURF 223.4740 2.2950 0.2295
G gas -52348.7552 69.0780 6.9078
G solv -6753.1118 42.4808 4.2481
TOTAL -59101.8670 63.9582 6.3958
Receptor:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -4572.1469 30.6590 3.0659
EEL -43902.0998 73.8516 7.3852
EGB -6541.0938 41.0578 4.1058
ESURF 217.0829 1.8461 0.1846
G gas -48474.2468 73.9029 7.3903
G solv -6324.0109 40.3857 4.0386
TOTAL -54798.2577 66.9648 6.6965
Ligand:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -280.7081 7.3213 0.7321
EEL -3240.3989 17.6030 1.7603
EGB -718.8419 9.9603 0.9960
ESURF 27.4207 0.3785 0.0378
G gas -3521.1070 18.3934 1.8393
G solv -691.4212 9.8387 0.9839
TOTAL -4212.5282 13.1081 1.3108
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -152.3314 6.1137 0.6114
EEL -201.0702 14.9502 1.4950
EGB 283.3499 13.6816 1.3682
ESURF -21.0296 0.6346 0.0635
DELTA G gas -353.4015 14.9217 1.4922
DELTA G solv 262.3203 13.3532 1.3353
DELTA TOTAL -91.0812 5.2328 0.5233
Glycosylated system:
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS 233341.9418 10755.6357 1075.5636
EEL -53088.9264 113.0561 11.3056
EGB -8052.1716 93.3975 9.3398
ESURF 275.1863 2.3094 0.2309
G gas 180253.0154 10737.1328 1073.7133
G solv -7776.9853 93.1892 9.3189
TOTAL 172476.0301 10746.3237 1074.6324
Receptor:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS 231218.9420 10732.6633 1073.2663
EEL -49673.8044 109.4603 10.9460
EGB -7577.2211 93.5891 9.3589
ESURF 268.6239 2.2230 0.2223
G gas 181545.1375 10716.4570 1071.6457
G solv -7308.5972 93.4285 9.3428
TOTAL 174236.5403 10725.5721 1072.5572
Ligand:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS 2272.6287 370.9014 37.0901
EEL -3199.4435 19.4181 1.9418
EGB -764.1110 12.0477 1.2048
ESURF 27.0960 0.3511 0.0351
G gas -926.8148 369.7865 36.9787
G solv -737.0149 11.9967 1.1997
TOTAL -1663.8297 370.3127 37.0313
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -149.6289 5.6904 0.5690
EEL -215.6785 20.3328 2.0333
EGB 289.1605 19.0056 1.9006
ESURF -20.5336 0.5990 0.0599
DELTA G gas -365.3074 20.9379 2.0938
DELTA G solv 268.6268 18.7488 1.8749
DELTA TOTAL -96.6805 6.8771 0.6877
-------------------------------------------------------------------------------
----------------------------------------------------
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Received on Thu Feb 06 2014 - 00:30:03 PST
