On Thu, Aug 30, 2012 at 12:33 PM, Sanjib Paul <sanjib88paul.gmail.com>wrote:
> Mr. Jason,
> Thank you very much. I followed what you told. I set
> environment variable http_proxy. Then give command
> $./patch_amber.py --update-tree
> Now, 21 bugfixes have been downloaded. Here, something "1 out of 1
> hunk failed....." is showing. Ignoring it I wrote in command line as
> given in http://jswails.wikidot.com/installing-amber12-and-ambertools-12
> ,
> $./configure gnu
> bash: ./configure: No such file or directory
>
This is a bad sign. Configure should be here, as long as you are in
$AMBERHOME.
> I am giving what I got after command $./patch_amber.py --update-tree.
> Please have a look.
> and let me know what I am doing wrong.
> $./patch_amber.py --update-tree
> Determining patches to download for AmberTools12
> Downloading bugfix.1
> Downloading bugfix.2
> Downloading bugfix.3
> Downloading bugfix.4
> Downloading bugfix.5
> Downloading bugfix.6
> Downloading bugfix.7
> Downloading bugfix.8
> Downloading bugfix.9
> Downloading bugfix.10
> Downloading bugfix.11
> Downloading bugfix.12
> Downloading bugfix.13
> Downloading bugfix.14
> Downloading bugfix.15
> Downloading bugfix.16
> Downloading bugfix.17
> Downloading bugfix.18
> Downloading bugfix.19
> Downloading bugfix.20
> Downloading bugfix.21
>
> Applying AmberTools12 patches
> Creating file
> /home/sanjib/amber12/AmberTools/src/parmed/ParmedTools/exceptions.py
> Creating file
> /home/sanjib/amber12/AmberTools/src/parmed/ParmedTools/gui/_guiactions.py
> Creating file
> /home/sanjib/amber12/AmberTools/src/parmed/chemistry/amber/mask.py
> Creating file
> /home/sanjib/amber12/AmberTools/src/parmed/chemistry/amber/readparm.py
> Creating file
> /home/sanjib/amber12/AmberTools/src/parmed/chemistry/exceptions.py
>
More bad news. patch_amber.py is located in $AMBERHOME, but it appears
like nothing else is. Configure can't be found. The Python modules listed
above are being created because patch_amber.py could not find them, but
they should already exist. As a result, patch_amber.py will not be able to
download or apply the patches.
My suggestion: erase your whole amber12 directory, download a fresh copy of
AmberTools12.tar.bz2 from
http://ambermd.org, and start over. If you still
have problems, report the *exact* commands you used as well as the error
messages. The information you gave here did not tell us how these files
could possibly be missing, so it's impossible for us to determine the
source of the problem.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 30 2012 - 10:30:05 PDT
