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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jan 27 2010 - 17:00:03 PST
