Re: [AMBER] Installation problem of AmberTools of AMBER11

From: Jason Swails <>
Date: Thu, 30 Aug 2012 10:34:55 -0400

On Thu, Aug 30, 2012 at 9:17 AM, Sanjib Paul <> wrote:

> Mr. Dac
> I also downloaded AmberTools12(using the "download
> AmberTools" link at . It is AmberTools12.tar.bz2.
> Then I proceed like following:
> $tar xvjf AmberTools12.tar.bz2.
> $cd amber12
> $export AMBERHOME =/home/sanjib/
> $./ --update-tree
> Error: No internet access!

 What this means is that tried to contact
http://ambermd.organd wasn't able to connect within 10 seconds. If
you know it takes longer
than that to contact, try:

./ --update-tree --timeout 20

That will make wait 20 seconds before giving up.

Another possibility is that you have to connect to the internet via a proxy
server -- do you know if this is the case? You can set the environment
variable http_proxy like so:

export http_proxy="http://username:password.proxyserver:port"

In this case, substitute your user name, password, the proxy server
address, and the port number (typically 800). I've done this, and it
allows to connect to and download updates.

But I have internet access. In webpage
> I have
> seen that patch_locs in should be changed from
> patch_locs = ['',
> '']
> to
> patch_locs = ['file:///path/to/mirror/folder/',
> 'file:///path/to/mirror/folder/']
> Here I can't understand what should I do? Please help.

This is what you should do if you absolutely *cannot* get to
contact to download the bug fixes. (Talk to your network
administrator for help). However, if it's absolutely impossible, what you
should do is set up the following folders in your home directory:


Then, download every bug fix for AmberTools 12 (from and put them in the
bugfixes/AmberTools/12.0 directory. If you have Amber 12, do the same
thing for Amber 12 (but put in the bugfixes/12.0 directory). After doing
this, you need to change the patch_locs line in like you
mentioned above. For example, if your home directory is /home/sanjib, then
those lines will become

patch_locs = ['file:///home/sanjib/bugfixes/AmberTools/12.0/',

This will tell to pull the files from your local filesystem
instead of the internet. Note, you will also have to comment out the
portion of the script that checks for internet access:

   # Make sure we have internet access, since we'll need it from now on
      amberhome = urlopen('')
      del amberhome
   except IOError, err:
      if 'timed out' in str(err):
         print >> sys.stderr, \
            'Error: Could not connect to in %.2f
seconds' % (
         print >> sys.stderr, 'Error: No internet access!'

This starts around line 828. (To comment it out, put a # at the beginning
of each line).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Aug 30 2012 - 08:00:04 PDT
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