Re: [AMBER] MMPBSA test fail

From: George Tzotzos <gtzotzos.me.com>
Date: Sat, 18 Dec 2010 14:10:58 +0100

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



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Received on Sat Dec 18 2010 - 05:30:04 PST
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