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
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Received on Sat Dec 18 2010 - 06:00:03 PST
