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
> > AMBER.ambermd.org
> > 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
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Received on Tue Sep 06 2011 - 05:00:03 PDT
