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 Mon Sep 05 2011 - 14:00:07 PDT
