On Thu, 2014-05-08 at 19:28 +0800, David Chen wrote:
> 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
This appears to be a single frame in which the van der Waals energy is
out of control. Look through the _MMPBSA_mutant_complex.mdout files and
try to find which frame it is. It may help visualizing the
corresponding _MMPBSA_mutant_complex.mdcrd file in VMD to try and find
the steric clash leading to this problem.
One solution would be to simply omit this frame from your analysis
(although it would be better to figure out why it appears to have been
corrupted).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 08 2014 - 05:00:03 PDT
