I'm not sure about your exact Amber organization and setup, but you say that
AMERHOME=/Users/george/Programs/amber11/
Yet, ptraj is being found here: /Users/tzotzos/Programs/amber11/bin/ptraj.
This appears to be finding a different Amber 11 installation than the one
that you say is AMBERHOME. Is sander found
in /Users/tzotzos/Programs/amber11/bin/ ? Do you have two different
AMBERHOME's defined somewhere?
There appears to be some sort of inconsistency in your environment.
I hope that helps.
-Bill
On Sat, Dec 18, 2010 at 8:10 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Apologies. Please find attached the mmpbsa.out file from the
> Generalized_Born test
>
> Thanks
>
> George
>
>
>
>
> On Dec 18, 2010, at 2:06 PM, George Tzotzos wrote:
>
> > Jason,
> >
> > Many thanks. Indeed I had untarred the mmpbsa_py.test.tar into a new
> directory in AMBERHOME.
> >
> > I did as per your suggestion and run the tests in both serial and
> parallel modes
> >
> > In both cases I have outputs indicating "file
> ddtmp.FINAL_RESULTS_MMPBSA.dat is short" (see end of this message)
> >
> > I moved into AMBERHOME/test/mmpbsa_py/01_Generalized_Born and executed
> the Run.GB script
> >
> > I'm attaching the output which indicates that sander is somehow missing
> despite the fact that AMBERHOME is set properly.
> >
> > george-Mac-Pro:01_Generalized_Born george$ echo $AMBERHOME
> > /Users/george/Programs/amber11/
> >
> > Any ideas on this?
> >
> > Many thanks for your help
> >
> > George
> >
> >
> >
> > ============================================================
> >
> > $ export DO_PARALLEL='mpirun -np 12'
> >
> > $ make test
> >
> > cd 01_Generalized_Born && ./Run.GB
> > cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> > diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> > file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> > PASSED
> > rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> > ==============================================================
> > cd 02_Poisson_Boltzmann && ./Run.PB
> > cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> > diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> > file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> > PASSED
> > rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> > ==============================================================
> > cd 03_Alanine_Scanning && ./Run.ALA
> > cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> > diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> > file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> > PASSED
> > rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> > ==============================================================
> >
> >
> > On Dec 18, 2010, at 1:39 AM, Jason Swails wrote:
> >
> >> Hello,
> >>
> >> My comments are placed below
> >>
> >> On Fri, Dec 17, 2010 at 2:07 PM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>
> >>> Sorry to come back on this one.
> >>>
> >>> mmpbsa_py george1$ make test
> >>>
> >>> produces the output below.
> >>>
> >>> I've checked the list and saw that this problem has been encountered
> >>> previously. However, I didn't find a satisfactory solution for my case.
> >>>
> >>> The weird thing is that the test produce outputs that appear to be OK.
> I'm
> >>> attaching an example for the NAB_Nmode test
> >>>
> >>>
> >>> I'm using Python 2.6.1
> >>>
> >>> I have installed AmberTools1.4 and amber11-parallel. I have no previous
> >>> installations of amber.
> >>>
> >>> Any clues how to solve this.
> >>>
> >>>
> >>> Thanks again
> >>>
> >>> George
> >>>
> >>>
> >>>
> >>>
> >>> cd 01_Generalized_Born && ./Run.GB
> >>> ./Run.GB: line 37: ../../dacdif: No such file or directory
> >>>
> >>
> >> It can't find dacdif, which is in $AMBERHOME/test. What this suggests
> is
> >> that the mmpbsa_py test directory is unpacked in the wrong place. This
> >> directory should be placed in $AMBERHOME/test.
> >>
> >> Be sure to follow all of the instructions here:
> >>
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htmincluding
> >> the instructions of where to place the files. This may also be
> >> why the nab_nmode script did not work (it has to be placed in
> $AMBERHOME/src
> >> in order for it to find the compilers).
> >>
> >> Good luck!
> >> Jason
> >>
> >>
> >> cd 02_Poisson_Boltzmann && ./Run.PB
> >>> ./Run.PB: line 37: ../../dacdif: No such file or directory
> >>> cd 03_Alanine_Scanning && ./Run.ALA
> >>> ./Run.ALA: line 42: ../../dacdif: No such file or directory
> >>> Mutant mdcrd can only be checked in serial
> >>> cd 04_Per_Residue_Decomp && ./Run.PerRes
> >>> ./Run.PerRes: line 40: ../../dacdif: No such file or directory
> >>> ./Run.PerRes: line 41: ../../dacdif: No such file or directory
> >>> cd 05_Pairwise_Decomp && ./Run.Pairwise
> >>> ./Run.Pairwise: line 40: ../../dacdif: No such file or directory
> >>> ./Run.Pairwise: line 41: ../../dacdif: No such file or directory
> >>> cd 06_NAB_Nmode && ./Run.nmode
> >>> ./Run.nmode: line 34: ../../dacdif: No such file or directory
> >>> cd 07_Comprehensive && ./Run.comprehensive
> >>> ./Run.comprehensive: line 71: ../../dacdif: No such file or directory
> >>> ./Run.comprehensive: line 72: ../../dacdif: No such file or directory
> >>> ./Run.comprehensive: line 73: ../../dacdif: No such file or directory
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sat Dec 18 2010 - 06:00:02 PST
