On Thu, Oct 10, 2013 at 11:25 PM, Terry M. Gray <grayt2.gmail.com> wrote:
> I'm trying to update a Mac OS X (10.6.8) AMBER installation from June 2012.
>
> AmberTools12 patches bugfix.12 through bugfix.22 were sucessfully applied.
>
> Applying AmberTools12 patches
> Error or warning during patching process for
> .patches/AmberTools_Unapplied_Patches/bugfix.23:
> Reversed (or previously applied) patch detected! Skipping patch.
> 15 out of 15 hunks ignored -- saving rejects to file
> AmberTools/src/configure2.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 6 out of 6 hunks ignored -- saving rejects to file
>
> AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 6 out of 6 hunks ignored -- saving rejects to file
>
> AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save.rej
> Reversed (or previously applied) patch detected! Skipping patch.
> 5 out of 5 hunks ignored -- saving rejects to file
> AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save.rej
>
It looks like these patches have already been applied, but have not been
registered. This can happen if you copy an Amber directory from one
location to another but not all files are copied, for instance. You can
try using the [--ignore-fails] command-line option to patch_amber.py to
have it push past these errors and apply what it can:
./patch_amber --update --ignore-fails
A (better) alternative is to download AmberTools 13 from the website and
install it alongside Amber 12. The updating script (update_amber) is a bit
more robust (although it still won't protect from the types of mistakes
that would cause this error).
HTH,
Jason
P.S. Please don't double-post questions, especially in the same day. We
answer them when we get a chance (and if the email comes after 5 or 6 pm
EST, it's likely to get answered the next morning, regardless of how many
times the inquiry is sent).
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 11 2013 - 04:30:05 PDT
