Hi,
It seems like the patch is having trouble finding where it is supposed
to apply itself. This can occur e.g. when patches are applied out of
order. The patch 'ptraj_2010-07-16-fixFilesize.patch' was an
unofficial bugfix; I recommend you use the release version of the
AmberTools 1.4 bugfixes (
http://ambermd.org/bugfixesat.html, use
bugfix.all) as well as a fresh copy of AmberTools 1.4 to ensure the
patches will be applied successfully. So do something like:
tar -zxf AmberTools.1.4.tgz (make sure you aren't overwriting your old
version of AmberTools 1.4)
cd amber11
patch -p0 -N < bugfix.all (Patching should have no issues at this point)
cd AmberTools/src
Then configure with whatever options are appropriate for your Mac and
compile normally. Let me know if you still have issues applying the
patch or problems with gzipped files after compilation.
-Dan
On Sun, Feb 6, 2011 at 12:51 PM, Kamali Sripathi <ksripath.umich.edu> wrote:
> Hi Dan and fellow AMBER users,
> I've been having similar problems with ptraj reading in gzipped trajectories
> after installing AmberTools v1.4 on my Mac. I've tried your most recent
> patch from July 18th, 2010, Dan, but I keep getting this message when I type
> in "patch -p0 -N < ptraj_2010-07-16-fixFilesize.patch":
> patching file AmberTools/src/ptraj/ptraj.c
> Hunk #1 FAILED at 2058.
> Hunk #2 FAILED at 2418.
> 2 out of 2 hunks FAILED -- saving rejects to file
> AmberTools/src/ptraj/ptraj.c.rej
> patching file AmberTools/src/ptraj/io.c
> Hunk #1 FAILED at 673.
> Hunk #2 FAILED at 698.
> Hunk #3 FAILED at 739.
> Hunk #4 FAILED at 766.
> Hunk #5 succeeded at 705 (offset -85 lines).
> Hunk #6 succeeded at 728 (offset -85 lines).
> 4 out of 6 hunks FAILED -- saving rejects to file
> AmberTools/src/ptraj/io.c.rej
> patching file AmberTools/src/ptraj/io.h
> Hunk #1 FAILED at 76.
> Hunk #2 FAILED at 97.
> 2 out of 2 hunks FAILED -- saving rejects to file
> AmberTools/src/ptraj/io.h.rej
> I think my problem may be more of a patching problem itself, or also the
> fact that I might not have compiled AmberTools properly, but I thought I'd
> start ask you, Dan, and Amber Mac users for a start.
> Thanks a lot, everyone!
> Kamali
>
>
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Received on Sun Feb 06 2011 - 12:00:04 PST
