Re: [AMBER] MMPBSA test fail

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 17 Dec 2010 20:31:26 +0100

Did as suggested

mmpbsa.out attached.

Thanks again

George





On Dec 17, 2010, at 8:16 PM, Bill Miller III wrote:

> The .save files are the files that the tests compare against. That file was
> made by us when we made the test suite. The files generated by the test will
> have not .save at the end of the filename. Did you download the test suite
> from the tutorial website, also? You should go into one of the directories
> in the test folder (for example, cd into 01_Generalized_Born) and try to
> execute the Run.GB script. Make sure to comment out the lines that remove
> the output files afterwards. Doing this should give us more information on
> the command line and/or in the output files that will be of help to pinpoint
> the potential problem.
>
> -Bill
>
>
> 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
>> 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
>>
>>
>>
>>
>>
>>
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>>
>>
>
>
> --
> 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 Fri Dec 17 2010 - 12:00:03 PST
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