Did you compile Amber in serial? MMPBSA.py.MPI uses sander, not sander.MPI.
So to run MMPBSA.py.MPI (or MMPBSA.py) you will need to compile Amber in
serial to get the proper sander executable.
-Bill
On Sat, Dec 18, 2010 at 9:11 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
> which sander returns nothing
>
> which sander.MPI returns /Users/tzotzos/Programs/amber11/bin/sander.MPI
>
> which sander.LES.MPI /Users/tzotzos/Programs/amber11/bin/sander.LES.MPI
>
> Anything missing in the installation of amber11?
>
>
>
> On Dec 18, 2010, at 2:49 PM, Bill Miller III wrote:
>
> > 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
> > _______________________________________________
> > 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 - 06:30:04 PST
