Dear amber users
I perfomed MM-gbsa calulations on protein-DNA complex with the input
startframe=45000, endframe=50000,interval=50,
verbose=2, keep_files=1,
/
&gb
igb=5,
energy parameters for one of the structure obtained during the minimization
process while calculating mm-gbsa for
complex
BOND = 4815.8916 ANGLE = 11390.0564 DIHED = 14813.1918
VDWAALS = -12637.6463 EEL = 76073.7556 EGB = -170810.8102
1-4 VDW = 5309.2638 1-4 EEL = -6615.7403 RESTRAINT = 0.0000
ESURF = 527.2730
Protein
BOND = 2410.1130 ANGLE = 6408.7585 DIHED = 8370.1630
VDWAALS = -6387.1198 EEL = -19155.5773 EGB = -38189.1432
1-4 VDW = 2839.4246 1-4 EEL = 18254.9688 RESTRAINT = 0.0000
ESURF = 283.1711
DNA
BOND = 2405.7787 ANGLE = 4981.2979 DIHED = 6443.0288
VDWAALS = -5361.2542 EEL = 284697.3736 EGB = -319646.0230
1-4 VDW = 2469.8392 1-4 EEL = -24870.7091 RESTRAINT = 0.0000
ESURF = 365.4367
*Delta*
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0001
0.0000
ANGLE 0.0000 0.0001
0.0000
DIHED 0.0000 0.0001
0.0000
VDWAALS -849.0947 21.1623
2.1057
EEL -189185.0199 479.2991
47.6920
1-4 VDW -0.0000 0.0001
0.0000
1-4 EEL -0.0000 0.0000
0.0000
EGB 186740.3398 462.6966
46.0400
ESURF -120.9537 1.5271
0.1520
DELTA G gas -190034.1146 479.3911
47.7012
DELTA G solv 186619.3860 462.5249
46.0229
DELTA TOTAL -3414.7286 39.9115
3.9713
In my case EGB is negative for free ligand (DNA), Protein and complex. EGB
negative implies soluble nature. But EEL is positive for complex and DNA.
What may be the reason for Positive EEL value of DNA (which is highly
negatively charged)
EGB is positive in Delta (does it imply insoluble nature of complex??)
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Received on Tue Apr 28 2015 - 11:30:02 PDT
