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
Received on Thu Nov 24 2011 - 09:00:03 PST
