On Sat, Dec 29, 2012 at 3:18 AM, BERGY <nucleic81.gmail.com> wrote:
> Hi Jason,
> i done all these procedure only after fresh install
> Does patching manually work patch -p0 -N < bugfix.X ??
>
This is exactly what patch_amber.py does. The main benefit of using
patch_amber.py is that it keeps track of which patches have been applied so
you always know the exact version you're using, and prevents you from
applying the same patches twice. (And, of course, it typically downloads
patches automagically and allows "configure" to update the distribution).
If patch_amber.py failed, then "patch -p0 -N < bugfix.X" will fail in the
same place as well. I've tested the current patches and patching system
pretty thoroughly, so I don't see any way of encountering these types of
problems unless:
1) You modified cpptraj and the patch conflicts with your changes
2) When you copied the patch files to your local repository, something went
wrong.
> > # ./patch_amber.py --patch-level
> > > Warning: Unknown number of bugfix .patches/Amber_Applied_Patches/bugfix
> > > (1).1
> > > Latest patch applied to AmberTools12: 15
> > > Latest patch applied to Amber12: 7
>
I missed this the first time. One of the file names you downloaded is
"bugfix (1).1", presumably because you downloaded it twice? Make sure that
all of the patch files are labeled "bugfix.#", the same as on the website.
Also, it may be worth asking your computer support staff how you should set
the variable "http_proxy" in order to get patch_amber.py to work. I've
gotten it to work behind a proxy before doing this, so I'm pretty sure it's
possible.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Dec 29 2012 - 12:00:04 PST
