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
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Received on Wed Jan 30 2013 - 04:30:03 PST
