Jason,
Just to clarify, I think the problem is "authenticated" proxies. I also
have had
no problem with my proxy setting the http_proxy environmental variable
but it seems Vaibhav's proxy requires username/password.
According to his e-mail he had the un/pwd set already.
>From what I gather in the docs urllib2 does support authenticated proxies.
On Wed, Jan 30, 2013 at 9:27 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Jan 30, 2013 at 12:27 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Daniel,
> > I have followed your suggestions and after making changes it is giving
> this
> > message below.
> > Did it apply patches correctly? I did not really understand the meaning
> of
> > the warning given below. It seems to have skipped some of the patchs, did
> > it? I have attached the patch_amber.py file, if check if it is according
> to
> > your expectation.
> >
>
> This is not right. Amber12 only has 14 patches. AmberTools 12 has 34.
> Therefore, it appears like you loaded /home/gm/bugfixes/12.0 with all of
> the AmberTools bug fixes. You need to be careful about putting the correct
> bug fixes in the correct directory. The error messages that appeared are
> fine -- it means that some patches were already applied (which makes sense,
> since AmberTools12 now ships with bug fixes 1-13). When you get your
> directories filled with the correct bug fixes, unpack a fresh version of
> Amber 12 and AmberTools 12 and try over (but make sure you keep your
> modified patch_amber.py).
>
> Also, while Dan said that the API documentation of urllib.urlopen does not
> technically support proxies, I've never had a problem connecting through a
> proxy by setting the http_proxy environment variable. If wget works,
> patch_amber.py should work, too. Perhaps a local sysadmin can help.
> Hopefully the next iteration of the updater will have better proxy
> support.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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
Received on Wed Jan 30 2013 - 05:00:03 PST
