Re: [AMBER] Amber 12 Updater error on Arch linux

From: Jason Swails <>
Date: Wed, 30 Oct 2013 07:20:18 -0400

On Wed, Oct 30, 2013 at 5:52 AM, M. Reza Ganjalikhany <> wrote:

> Dear Amber Users,
> I am trying to compile Amber 12 on Arch linux (latest kernel 3.11.6), but I
> get the error message from the biginig when updater tries to autoupdate
> Amber as below. Also, the rest of check points pass successfully at
> configuration step.
> Any help will be greatly appreciated,
> [root.localhost amber12]# ./configure gnu
> Checking for updates...
> File "./update_amber", line 30
> except AmberUpdaterError, err:
> ^
> SyntaxError: invalid syntax

This is valid syntax for Python 2, but not for Python 3. We are reaching a
point where newer Linux distributions are starting to finally retire Python
2 as their main system Python and they are moving to Python 3. According
to the Arch Linux Wiki, Python 3 is now the default Python version shipped
with that Linux distribution. Because Python 2.4 is still a commonly-used
default Python version on RHEL 5 -- which is still popular for some larger
clusters -- it was important for update_amber to support Python 2.4 through
2.7 (but at the time of writing, no distros had fully switched to Python
3). The upcoming AmberTools 14 will feature an update_amber that uses
syntax fully compatible with both Python 2 (2.4+) and Python 3
(significantly trickier than it would seem). For the time being, though,
Python 2 is required for AmberTools 13's updating script.

Long story short, change the shebang line of update_amber from

#!/usr/bin/env python


#!/usr/bin/env python2

See the Arch Linux wiki page on Python for more information:


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Oct 30 2013 - 04:30:03 PDT
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