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
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Received on Sat Dec 18 2010 - 06:30:03 PST
