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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>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Tue Sep 06 2011 - 01:30:04 PDT
