That seems fine to me. Does `which sander` respond with the correct location
of your sander executable? Because if sander is found in a directory in your
path (like $AMBERHOME/bin), then MMPBSA.py and MMPBSA.py.MPI should be able
to find it.
-Bill
On Sat, Dec 18, 2010 at 8:40 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thanks Bill,
>
> I'm setting AMBERHOME as follows:
>
> export PATH=/Users/tzotzos/Programs/amber11/bin
> export AMBERHOME=/Users/tzotzos/Programs/amber11
>
> Is there any inconsistency there?
>
> George
>
>
> On Dec 18, 2010, at 2:24 PM, Bill Miller III wrote:
>
> > I'm not sure about your exact Amber organization and setup, but you say
> that
> > AMERHOME=/Users/george/Programs/amber11/
> >
> > Yet, ptraj is being found here:
> /Users/tzotzos/Programs/amber11/bin/ptraj.
> > This appears to be finding a different Amber 11 installation than the one
> > that you say is AMBERHOME. Is sander found
> > in /Users/tzotzos/Programs/amber11/bin/ ? Do you have two different
> > AMBERHOME's defined somewhere?
> >
> > There appears to be some sort of inconsistency in your environment.
> >
> > I hope that helps.
> >
> > -Bill
> >
> >
> > On Sat, Dec 18, 2010 at 8:10 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Apologies. Please find attached the mmpbsa.out file from the
> >> Generalized_Born test
> >>
> >> Thanks
> >>
> >> George
> >>
> >>
> >>
> >>
> >> On Dec 18, 2010, at 2:06 PM, George Tzotzos wrote:
> >>
> >>> Jason,
> >>>
> >>> Many thanks. Indeed I had untarred the mmpbsa_py.test.tar into a new
> >> directory in AMBERHOME.
> >>>
> >>> I did as per your suggestion and run the tests in both serial and
> >> parallel modes
> >>>
> >>> In both cases I have outputs indicating "file
> >> ddtmp.FINAL_RESULTS_MMPBSA.dat is short" (see end of this message)
> >>>
> >>> I moved into AMBERHOME/test/mmpbsa_py/01_Generalized_Born and executed
> >> the Run.GB script
> >>>
> >>> I'm attaching the output which indicates that sander is somehow missing
> >> despite the fact that AMBERHOME is set properly.
> >>>
> >>> george-Mac-Pro:01_Generalized_Born george$ 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
> > _______________________________________________
> > 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 - 06:00:03 PST
