Yup, that fixed it. Thanks Bill!
Jesper
Den 06/09/2011 kl. 04.31 skrev Bill Miller III:
> I have never seen this exact error before, but I have seen similar errors.
> Hopefully upgrading to the AT 1.5 version fixes the issue.
>
> -Bill
>
> 2011/9/6 Jesper Sørensen <lists.jsx.dk>
>
>> Thanks Bill.
>> I am running the calculation again with AT1.5 - that was just a blunder on
>> my part using an old installation on the cluster.
>> I have also added the keep_files=2 in my input file.
>>
>> Is the below error one you have encountered before?
>> I will send you an update once the calculations finish again.
>>
>> Best,
>> Jesper
>>
>>
>> Den 05/09/2011 kl. 13.53 skrev Bill Miller III:
>>
>>> To not remove the temporary files at the end of the calculation, you
>> should
>>> set keep_files=2 in the &gen section of the mmpbsa.in file. I would also
>>> advise that you upgrade to AmberTools 1.5 which is the most up-to-date
>>> version of MMPBSA.py. There have been several updates (including to
>>> decomposition analysis) to MMPBSA.py in the new release.
>>>
>>> -Bill
>>>
>>> 2011/9/5 Jesper Sørensen <lists.jsx.dk>
>>>
>>>> Hi all,
>>>>
>>>> I am running an alanine scanning calculation and I am getting the
>> following
>>>> error:
>>>>
>>>> [jesper.fe2 BOV-BOV_ALA_221LYS_ALA_245GLU]$ more 2xALA_SCAN.e820147
>>>> Warning: igb=5 should be used with either mbondi2 or bondi pbradii set.
>>>> Yours are modified Bondi radii (mbondi)
>>>> cat: _MMPBSA_mutant_complex_pb.mdout.22: No such file or directory
>>>> rm: cannot remove `_MMPBSA_mutant_complex_pb.mdout.22': No such file or
>>>> directory
>>>> Traceback (most recent call last):
>>>> File "/com/amber/amber11/bin/MMPBSA.py.MPI", line 1571, in <module>
>>>> decompout, idecomp, dec_verbose, ligstart, decomprun, surften,
>>>> cavity_surften, temp)
>>>> File "/home/com/amber/NEW/amber11/src/mmpbsa_py/utils.py", line 4664, in
>>>> PrintFinalResults
>>>>
>>>>
>> mutstring,finaloutput,mutstring,numframes,sander_apbs,one_trajectory,verbose)
>>>> File "/home/com/amber/NEW/amber11/src/mmpbsa_py/utils.py", line 2180, in
>>>> pboutput
>>>> bonddif[x] = bonddif[x] - bond[x]
>>>> IndexError: list index out of range
>>>>
>>>> Is there a way that I can get MMPBSA not to delete the files at the end
>> -
>>>> so that I can see if "_MMPBSA_mutant_complex_pb.mdout.22" actually does
>> not
>>>> exist?
>>>> Also, any clues why this file is not created?
>>>>
>>>> Best,
>>>> Jesper
>>>>
>>>>
>>>> _______________________________________________
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>>>> 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
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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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 Tue Sep 06 2011 - 12:30:03 PDT
