The part of the file that you have shown is exactly what you should get.
Those numbers are identical to the values you should be getting with a
proper installation. However, without seeing the entire
FINAL_RESULTS_MMPBSA.dat.dif, we cannot tell if there is an error in another
part of the file or not.
-Bill
On Wed, Jan 27, 2010 at 7:53 PM, Christine Baranski <
chbaranski.googlemail.com> wrote:
> Dear Miller
>
> Thanks for reply. Yes it seems that
>
> < WARNINGS:
> < igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are
> modified Bondi radii (mbondi)
>
> is the only warning
>
> Here are a selection last few lines from the file
> FINAL_RESULTS_MMPBSA.dat.dif
>
> <
>
> -------------------------------------------------------------------------------
> < VDWAALS -1954.7302 4.0135
> 2.3172
> < EEL -17013.6292 56.4968
> 32.6184
> < EPB -3149.5365 19.7006
> 11.3742
> < ECAVITY 69.0143 0.2638
> 0.1523
> < TOTAL -10654.6452 28.6094
> 16.5177
> < Ligand:
> < Energy Component Average Std. Dev. Std. Err. of
> Mean
> <
>
> -------------------------------------------------------------------------------
> < VDWAALS -2.2229 1.1148
> 0.6436
> < EEL -5.2403 1.0202
> 0.5890
> < EPB -36.8878 1.6083
> 0.9286
> < ECAVITY 3.2833 0.0084
> 0.0048
> < TOTAL -37.0151 0.5880
> 0.3395
> < Differences (Complex - Receptor - Ligand):
> < Energy Component Average Std. Dev. Std. Err. of
> Mean
> <
>
> -------------------------------------------------------------------------------
> < VDWAALS -58.0643 4.3366
> 2.5037
> < EEL -37.2044 2.2074
> 1.2744
> < EPB 62.4453 2.9759
> 1.7181
> < ECAVITY -4.8321 0.1006
> 0.0581
> < DELTA G binding = -37.6555 +/- 1.5219
> 0.8787
> < RESULT OF ALANINE SCANNING: (D231A MUTANT:) DELTA DELTA G binding =
> 0.2565 +/- 0.1727
> <
>
> -------------------------------------------------------------------------------
> <
>
> -------------------------------------------------------------------------------
> < WARNINGS:
> < igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are
> modified Bondi radii (mbondi)
>
>
>
>
>
>
>
> 2010/1/28 Billy Miller III <brmilleriii.gmail.com>
>
> > This warning is expected as the system was created with mbondi radii
> before
> > igb=5 was being used for these calculations. If this is the only error
> > message in FINAL_RESULTS_MMPBSA.dat.dif, then the installation was
> > successful.
> >
> > Good luck!
> >
> > -Bill Miller
> >
> > On Wed, Jan 27, 2010 at 7:08 PM, Christine Baranski <
> > chbaranski.googlemail.com> wrote:
> >
> > > Dear All,
> > >
> > > Here is a copy of my screen outputs
> > >
> > >
> > > system:test user2$ make -f Makefile_at test.mmpbsa
> > > cd mmpbsa_py && ./Run
> > > This test will take awhile. Please be patient.
> > > diffing mutant_complex.mdcrd.save with _MMPBSA_mutant_complex.mdcrd
> > > PASSED
> > > ==============================================================
> > > diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> > > possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
> > > ==============================================================
> > > system:test user2$ cd mmpbsa_py
> > > system:mmpbsa_py user2$ more FINAL_RESULTS_MMPBSA.dat.dif
> > >
> > >
> > > the last line to this file is
> > >
> > > igb=5 should be used with either mbondi2 or bondi pbradii set. Yours
> are
> > > modified Bondi radii (mbondi)
> > >
> > >
> > >
> > > Please suggest something in this regards. I have already updated all
> > bugs.
> > > _______________________________________________
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> > >
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> >
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Received on Wed Jan 27 2010 - 17:30:03 PST
