Thank you very much!
On Thu, Nov 24, 2011 at 11:45 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Yes, those diffs are fine.
>
> All the best,
> Jason
>
> On Thu, Nov 24, 2011 at 7:57 AM, co nguyentruong <nguoithamdo.gmail.com
> >wrote:
>
> > Dear
> >
> > Thank you very much, but how about this test:
> >
> > Possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
> > /export/apps/amber111.4/test/mmpbsa_py
> > 99c99
> > < EPB -3305.9807 18.9403
> > 13.3928
> > ---
> > > EPB -3305.9472 18.9343
> > 13.3886
> > 102,103c102,103
> > < G solv -3238.4981 18.9458
> > 13.3967
> > < TOTAL -22209.0959 20.7614
> > 14.6805
> > ---
> > > G solv -3238.4646 18.9399
> > 13.3925
> > > TOTAL -22209.0624 20.7673
> > 14.6847
> > 109c109
> > < EPB -3330.8514 16.7749
> > 11.8617
> > ---
> > > EPB -3330.9587 16.9716
> > 12.0007
> > 112,113c112,113
> > < G solv -3261.8320 16.7782
> > 11.8640
> > < TOTAL -22129.0486 21.4524
> > 15.1691
> > ---
> > > G solv -3261.9392 16.9749
> > 12.0031
> > > TOTAL -22129.1559 21.2557
> > 15.0300
> > 119c119
> > < EPB -35.6427 0.7251
> > 0.5128
> > ---
> > > EPB -35.6425 0.7250
> > 0.5127
> > 122,123c122,123
> > < G solv -32.3630 0.7252
> > 0.5128
> > < TOTAL -40.8940 2.5242
> > 1.7849
> > ---
> > > G solv -32.3629 0.7251
> > 0.5127
> > > TOTAL -40.8938 2.5240
> > 1.7848
> > 129c129
> > < EPB 60.5134 1.4402
> > 1.0184
> > ---
> > > EPB 60.6541 1.2377
> > 0.8752
> > 132,133c132,133
> > < DELTA G solv 55.6968 1.4468
> > 1.0231
> > < DELTA G binding = -39.1533 +/- 1.8331
> > 1.2962
> > ---
> > > DELTA G solv 55.8376 1.2454
> > 0.8806
> > > DELTA G binding = -39.0126 +/- 2.0356
> > 1.4394
> > 143c143
> > < EPB -3117.8743 24.7574
> > 17.5061
> > ---
> > > EPB -3117.8429 24.7544
> > 17.5040
> > 146,147c146,147
> > < G solv -3050.4486 24.7620
> > 17.5093
> > < TOTAL -22126.5624 20.9106
> > 14.7861
> > ---
> > > G solv -3050.4172 24.7590
> > 17.5072
> > > TOTAL -22126.5310 20.9136
> > 14.7882
> > 153c153
> > < EPB -3142.7956 22.7384
> > 16.0785
> > ---
> > > EPB -3142.7532 22.7234
> > 16.0679
> > 156,157c156,157
> > < G solv -3073.8330 22.7411
> > 16.0804
> > < TOTAL -22046.9596 21.4998
> > 15.2027
> > ---
> > > G solv -3073.7906 22.7261
> > 16.0698
> > > TOTAL -22046.9172 21.5149
> > 15.2133
> > 163c163
> > < EPB -35.6427 0.7251
> > 0.5128
> > ---
> > > EPB -35.6425 0.7250
> > 0.5127
> > 166,167c166,167
> > < G solv -32.3630 0.7252
> > 0.5128
> > < TOTAL -40.8940 2.5242
> > 1.7849
> > ---
> > > G solv -32.3629 0.7251
> > 0.5127
> > > TOTAL -40.8938 2.5240
> > 1.7848
> > 173c173
> > < EPB 60.5639 1.2938
> > 0.9148
> > ---
> > > EPB 60.5529 1.3060
> > 0.9235
> > 176,177c176,177
> > < DELTA G solv 55.7474 1.3011
> > 0.9200
> > < DELTA G binding = -38.7089 +/- 1.9350
> > 1.3683
> > ---
> > > DELTA G solv 55.7364 1.3133
> > 0.9286
> > > DELTA G binding = -38.7200 +/- 1.9228
> > 1.3596
> > 180c180
> > < RESULT OF ALANINE SCANNING: (D231A MUTANT:) DELTA DELTA G binding =
> > 0.4443 +/- 2.6654
> > ---
> > > RESULT OF ALANINE SCANNING: (D231A MUTANT:) DELTA DELTA G binding =
> > 0.2926 +/- 2.8001
> >
> > Do you think it safe for running?
> >
> > With my best regard
> >
> > Co
> >
> > On Thu, Nov 24, 2011 at 1:21 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > These are expected. The end of the log of AT15_Amber11.py says this:
> > >
> > > NOTE: Because PBSA has changed since Amber 11 was released, some
> > > tests are known to fail and others are known to quit in error. These
> > > can be safely ignored.
> > >
> > > Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc
> > > Run.argasp.min Run.dadt.min Run.dgdc.min
> > > Run.lysasp.min Run.polyALA.min Run.polyAT.min
> > > Run.argasp.min Run.dadt.min Run.dgdc.min
> > > Run.lysasp.min Run.polyALA.min Run.polyAT.min
> > > Run.argasp.min Run.dadt.min Run.dgdc.min
> > > Run.lysasp.min Run.polyALA.min Run.polyAT.min
> > >
> > > Tests that produce possible FAILUREs:
> > > cd sander_pbsa_ipb2 && ./Run.110D.min
> > > cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail
> > here)
> > > cd sander_pbsa_tsr && ./Run.tsrb.min
> > > cd sander_pbsa_decres && ./Run.pbsa_decres
> > > mm_pbsa.pl tests 02, 03, and 05
> > >
> > > HTH,
> > > Jason
> > >
> > > On Wed, Nov 23, 2011 at 4:16 AM, co nguyentruong <
> nguoithamdo.gmail.com
> > > >wrote:
> > >
> > > > Sorry all, i forgot to attach logs file.
> > > >
> > > >
> > > > On Wed, Nov 23, 2011 at 4:14 PM, co nguyentruong <
> > nguoithamdo.gmail.com
> > > > >wrote:
> > > >
> > > > > Dear
> > > > >
> > > > > we set up serial and parallel of two Amber11 versions in rock 5.4
> > and
> > > > > compiler is gcc-4-4 and use mpich for parallel installation . The
> > first
> > > > one
> > > > > is version of Amber 11 and AmberTool 1.4 and second one is Amber11
> > and
> > > > > AmberTool 1.5. Their names are Amber1114 and Amber11_1.5
> > respectively.
> > > > > However, while almost of tests of Amber1114 got one possible
> failure,
> > > > > Amber11_1.5 got more possible failures. I attached log file of
> their
> > > test
> > > > > on our cluster. And some users bothered that my amber set up is not
> > > > > reliable. Should we use these installation for running ?
> > > > >
> > > > > Thank you very much
> > > > >
> > > > > Nguyen Truong Co
> > > > >
> > > > > Institute for Computational Science and Technology
> > > > >
> > > > > Ho Chi Minh City Viet Nam
> > > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Nov 24 2011 - 12:00:05 PST
