Sorry, I missed this email before.
On Thu, Feb 6, 2014 at 3:11 AM, Maryam Azimzadeh Irani <
maryamai.bii.a-star.edu.sg> wrote:
>
>
> 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
>
This seems unusual. It seems like there might be a couple frames that have
bad van der Waals clashes. You can use the -eo flag to dump the energies
for every frame to see which frames are problematic. Visualizing these
frames might help you determine why this happened. Indeed, a couple bad
clashes will ruin an average.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 10:00:02 PST
