The line that exits due to lack of connection is "sys.exit(1)" around line
number 865 in patch_amber.py as shown at the end of this message.
But I don't know if it will run fine just because the exit line is
commented out.
According to the documentation of urllib.urlopen (which is what
patch_amber.py is using):
"Proxies which require authentication for use are not currently supported;
this is considered an implementation limitation."
This is probably why you cannot download the patches using your
authentication-based proxy.
Code below:
# Make sure we have internet access, since we'll need it from now on
try:
amberhome = urlopen('
http://ambermd.org')
amberhome.close()
del amberhome
except IOError, err:
if 'timed out' in str(err):
print >> sys.stderr, \
'Error: Could not connect to http://ambermd.org in %.2f
seconds' % (
opt.timeout)
else:
print >> sys.stderr, 'Error: No internet access!'
sys.exit(1)
On Wed, Jan 30, 2013 at 1:55 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote:
> Dear Daniel,
> Thank for your reply.
> Yes, wget works, using wget only I have downloaded the patches manually in
> the folder as suggested by Jason here
> http://archive.ambermd.org/201208/0427.html
> But then I could not figure out myself which lines in the patch_amber.py
> script to comment-out?
> As far as I'm able to understand proxy setting are fine (I'm able to access
> my email and use wget).
> Please suggest.
>
> On Wed, Jan 30, 2013 at 10:01 AM, Daniel Sindhikara <sindhikara.gmail.com
> >wrote:
>
> > Does wget or curl work for you in the terminal? If not you should contact
> > your sysadmin to help you with the proxy settings.
> >
> > -Dan
> >
> >
> > On Wed, Jan 30, 2013 at 1:03 PM, Vaibhav Dixit <vaibhavadixit.gmail.com
> > >wrote:
> >
> > > Please suggest on this patching problem, I'm unable to install Amber12.
> > > Thanks in advance.
> > >
> > > On Tue, Jan 29, 2013 at 9:49 AM, Vaibhav Dixit <
> vaibhavadixit.gmail.com
> > > >wrote:
> > >
> > > > Dear Amber community members,
> > > > I'm facing a problem while patching amber12 updates using the command
> > > > ---------
> > > > gm.linux-rfml:/usr/local/amber12> ./patch_amber.py --update-tree
> > > > Error: No internet access!
> > > > -----------
> > > > I tried suggestions given here,
> > > > http://archive.ambermd.org/201208/0427.html
> > > >
> > > > My proxy setting are correct (I'm able to use internet on the same PC
> > and
> > > > I have set the path with proper user name and password (export
> > > http_proxy="
> > > > http://username:password.proxy.iisc.ernet.in:3128"). But this did
> not
> > > > work, then I tried *./patch_amber.py --update-tree --timeout 20, but
> > this
> > > > also gave the same result*
> > > >
> > > > After downloading all the patches, I have made following changes to
> the
> > > > patch_amber.py file, *but I'm unable to understand which line in this
> > > > file should I comment out*, so that the patch file are used directly
> > from
> > > > the folder specified.
> > > > -----------
> > > > BUGFIX_PREFIX = 'bugfix'
> > > > patch_locs = ['file:///home/gm/bugfixes/AmberTools/12.0/',
> > > > 'file:///home/gm/bugfixes/12.0/']
> > > > -----------
> > > >
> > > > --
> > > > With regards
> > > >
> > > > Dr. Dixit Vaibhav Anil (Dr. D.S.Kothari Fellow)
> > > > Department of Inogranic and Physical Chemistry
> > > > Indian Institute of Science (IISc), Bangalore-560012
> > > > Karnataka.
> > > > Phone (Mobile): +919915214408, +91-7709129400.
> > > > E-mail: vaibhavadixit.gmail.com, vaibhavadixit.ipc.iisc.ernet.in
> > > > http://www.iisc.ernet.in/
> > > > <http://www.niper.nic.in>
> > >
> > >
> > >
> > >
> > > --
> > > With regards
> > >
> > > Vaibhav A. Dixit
> > > Ph.D.
> > > Department of Medicinal Chemistry
> > > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > > Punjab -160 062 INDIA
> > > Phone (Mobile): +919915214408, +91-7709129400.
> > > E-mail: vaibhavadixit.gmail.com
> > > www.niper.nic.in
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
> > Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
> > sindhikara.gmail.com <http://www.dansindhikara.com>
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D.
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408, +91-7709129400.
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
sindhikara.gmail.com <http://www.dansindhikara.com>
--
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AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 29 2013 - 21:30:02 PST
