Re: [AMBER] abertools12 installation failure

From: Francesco Pietra <>
Date: Sun, 15 Apr 2012 19:07:45 +0200

Hi Jason:
Thanks for the immediate reply, Sunday notwithstanding.

It seems that the patch file needs a correction:

Fatal error: Badly formatted patch file configure.patch. Could not
find end of header.

If relevant, in order to have the latest nvidia drivers, I am using
the testing version of Debian amd64, python version 2.6.7. Apart from
that, in a testing version, bugs that can last a few days can't be
ruled out.

francesco pietra

On Sun, Apr 15, 2012 at 5:22 PM, Jason Swails <> wrote:
> On Sun, Apr 15, 2012 at 3:53 AM, Francesco Pietra <>wrote:
>> Hello:
>> Under Debian GNU-Linux amd64, having amber10 and an installation of
>> ambertools1.5, I was trying to install ambertools12, wishing to have
>> xleap.
>> Recreated .bashrc for ambertools12/amber10, I got errors at
>> ./configure gnu
>> ...
>> Downloading bugfix.1
>> Applying AmberTools12_patches
>> Moving bugfix.1 to AmberTools_Applied_Patches
>> ERROR: the X11 libraries are not in the usual location!
> I believe I see the issue.  It has to do with the fact that the configure
> script only looks for the static Xt library, when you probably only have
> the shared lib.  To clarify -- the configure script *does* look in
> /usr/lib/x86_64-linux-gnu -- just not for the shared objects.  I've
> attached a patch that should fix your issue (please let me know if it does).
> You can apply the patch using from $AMBERHOME:
> ./ --apply configure.patch
> To this concern I dare saying that Debian users are currently
>> threatened by developers of Linux applications referreing to Ubuntu
>> and never to debian. actually, Ubuntu is taking Debian, introducing
>> some bugs, and then having gained the media.
> Ubuntu is easier to install and deploy than most other distros (especially
> Debian), so addressing Ubuntu directly reaches more people.  It's one of
> the sacrifices we have to make to avoid using Ubuntu (and the horrible
> Unity).
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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Received on Sun Apr 15 2012 - 10:30:02 PDT
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