On Thu, Sep 5, 2013 at 3:30 PM, Robyn Ayscue <robyn.ayscue.gmail.com> wrote:
> Greetings all,
>
> I've been trying to apply bugfixes to Amber11 (running on a 64-bit Linux
> machine / Fedora 17), and the update_amber script insists that we have
> Amber12. I'm positive that we don't have Amber12, yet the version number
> reported back to me when I type "update_amber --version" at a bash prompt
> is "Amber 12.01". Unless someone broke into our lab and surreptitiously
> installed Amber12 on our machines here (and for free, no less!), I'm pretty
> sure the update_amber script is mistaken. Has anyone else run into this
> phenomenon?
>
The only way you could have an update_amber script in your Amber 11
directory is either by
1) Forcibly untarring an AmberTools 13 tarball (which unpacks into
amber12/) and an Amber 11 tarball (which unpacks into amber11) into the
same place by switching the directory name out from under one of the two
packages.
2) Unpacking an AmberTools 13 tarball and copying the update_amber script
from the amber12 directory to the amber11 directory where you unpacked
Amber11.tar.bz2.
If you did (1), then I'm sorry to report that AmberTools 13 and Amber 11
are incompatible, and they must remain in different locations. See this
page for instructions on installing Amber 11 with a 'new' AmberTools:
http://jswails.wikidot.com/installing-ambertools-13-and-older-amber
If you did (2), then I'm sorry to report that update_amber is not
relocatable. Version numbers are hard-coded. Also, update_amber was
introduced with Amber and AmberTools version 12 (it was called
'patch_amber.py' back then). The patching process of AmberTools 1.5 and
Amber 11 was so complex as to be unsupportable via the mechanism coded into
update_amber, so I made no attempt to back-port it to Amber 11. If you
must use Amber 11 and cannot upgrade, then you'll have to apply all patches
and bugfixes the 'old-fashioned' way.
See the instructions here:
http://jswails.wikidot.com/installing-amber11-and-ambertools-1-5
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 05 2013 - 13:00:04 PDT
