On Tue, Apr 28, 2015 at 2:03 PM, Muthukumaran R <kumaran.bicpu.edu.in>
wrote:
> 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,
>
This is an incomplete input file that shouldn't run in MMPBSA.py.
Assuming that you had &general at the top and a / closing the &gb namelist,
it would work.
> 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)
>
Because it is highly negatively charged. Like charges repel (and are
unfavorable), so DNA interacting with itself is highly unfavorable in the
gas phase assuming deprotonated phosphates. Solvation forces mitigate this
unfavorable interaction (which is why EGB will be negative for the free
DNA). EGB often offsets EEL.
EGB is positive in Delta (does it imply insoluble nature of complex??)
>
No, simply that the complex is less soluble than the separate protein and
DNA. Which shouldn't come as much of a surprise given the high solubility
of DNA.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 28 2015 - 12:00:03 PDT
