[AMBER] problem in installing AmberTools13

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Tue, 3 Sep 2013 07:36:50 +0100 (BST)

I am trying to  install AMBERTOOLS13. So I downloaded AmberTools13 and unzip. Then I updated first time by running the script  "update_amber". I ran the same script again. I get this message below:

Preparing to apply updates... please wait.
Downloading updates for AmberTools 13
Downloading AmberTools 13/update.1 (14.25 KB)
Applying AmberTools 13/update.1
Downloading AmberTools 13/update.2 (1.99 KB)
Applying AmberTools 13/update.2
Downloading AmberTools 13/update.3 (39.60 KB)
Applying AmberTools 13/update.3
Downloading AmberTools 13/update.4 (602.14 KB)
Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0% Done.
Applying AmberTools 13/update.4
Downloading AmberTools 13/update.5 (35.79 KB)
Applying AmberTools 13/update.5
Downloading AmberTools 13/update.6 (4.83 KB)
Applying AmberTools 13/update.6
Downloading AmberTools 13/update.7 (949 Bytes)
Applying AmberTools 13/update.7

updater.py has found a patch to itself... I am quitting now so
future updates will apply with the fixed script.

Run this script again to get all updates.

[root.glycogpu amber12]# ./update_amber --update

Preparing to apply updates... please wait.
Traceback (most recent call last):
  File "./update_amber", line 23, in <module>
  File "/usr/local/apps/amber12/updateutils/main.py", line 477, in mainloop
  File "/usr/local/apps/amber12/updateutils/main.py", line 43, in newfcn
    fcn(self, *args, **kwargs)
  File "/usr/local/apps/amber12/updateutils/main.py", line 308, in update
  File "/usr/local/apps/amber12/updateutils/main.py", line 43, in newfcn
    fcn(self, *args, **kwargs)
  File "/usr/local/apps/amber12/updateutils/main.py", line 208, in _update_ambertools
  File "/usr/local/apps/amber12/updateutils/main.py", line 43, in newfcn
    fcn(self, *args, **kwargs)
  File "/usr/local/apps/amber12/updateutils/main.py", line 186, in _update_tree
    last = remote.last()
  File "/usr/local/apps/amber12/updateutils/repos.py", line 289, in last
  File "/usr/local/apps/amber12/updateutils/downloader.py", line 98, in new_fcn
    return fcn(*args, **kwargs)
  File "/usr/local/apps/amber12/updateutils/repos.py", line 204, in fill_list
    p = urlopen(url)
  File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen
    return _opener.open(url, data, timeout)
  File "/usr/lib64/python2.6/urllib2.py", line 391, in open
    response = self._open(req, data)
  File "/usr/lib64/python2.6/urllib2.py", line 409, in _open
    '_open', req)
  File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
    result = func(*args)
  File "/usr/lib64/python2.6/urllib2.py", line 1190, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open
    raise URLError(err)
urllib2.URLError: <urlopen error timed out>

What does this means? 
Is anything wrong in the installation?

Please help.

Thank you.

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Received on Tue Sep 03 2013 - 00:00:02 PDT
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