[AMBER] update Ambertools 12 to 13 fails

From: Robert Wohlhueter <bobwohlhueter.earthlink.net>
Date: Sat, 06 Jul 2013 17:08:46 -0400

I do have AmberTools 12 installed (on an Ubuntu 12.04 AMD 64-bit
machine), and just now patched through bugfix.37 (successfully, I think,
but I haven't try to rebuild yet.)

The problem is that when I try the quick-and-easy `update_amber
--upgrade` I get some fairly opaque error messages (copied below), which
I take to mean AmberTools 12 is not really upgraded to 13, and therefore
not ready to rebuild.

Any advice? I haven't made custom changes to the Amber Tools 12 source
code, but should I follow the script's advice and download the

Bob Wohlhueter


root.winter-linux: ...lib/amber12 (337%)# ./update_amber --upgrade
./update_amber --upgrade
You are about to perform a major upgrade. This is NOT reversible.

Do you wish to continue? (y/N) y
Reversing Amber 12/bugfix.18
Reversing Amber 12/bugfix.17
Reversing Amber 12/bugfix.16
If the upgrade attempt fails, or you have made any custom changes
to the AmberTools source code, please download the AmberTools13
tarball from http://ambermd.org/AmberTools-get.html

NOTE: This upgrade cannot be reversed!
Downloading upgrade.patch.bz2 (23.88 MB)
Downloading: [ ] 1.9%Traceback (most recent call last):
   File "./update_amber", line 23, in <module>
   File "/usr/local/lib/amber12/updateutils/main.py", line 483, in mainloop
   File "/usr/local/lib/amber12/updateutils/main.py", line 43, in newfcn
     fcn(self, *args, **kwargs)
   File "/usr/local/lib/amber12/updateutils/main.py", line 369, in
   File "/usr/local/lib/amber12/updateutils/upgrade.py", line 196, in
     if self._apply_upgrade_patch():
   File "/usr/local/lib/amber12/updateutils/downloader.py", line 98, in
     return fcn(*args, **kwargs)
   File "/usr/local/lib/amber12/updateutils/upgrade.py", line 160, in
   File "/usr/local/lib/amber12/updateutils/downloader.py", line 152, in
   File "/usr/lib/python2.7/socket.py", line 380, in read
     data = self._sock.recv(left)
   File "/usr/lib/python2.7/httplib.py", line 561, in read
     s = self.fp.read(amt)
   File "/usr/lib/python2.7/socket.py", line 380, in read
     data = self._sock.recv(left)
socket.timeout: timed out
root.winter-linux: ...lib/amber12 (338%)#

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Received on Sat Jul 06 2013 - 14:30:03 PDT
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