Re: [AMBER] Installation problem of AmberTools of AMBER11

From: Sanjib Paul <>
Date: Fri, 31 Aug 2012 00:28:38 +0530

Hello Mr.Jason,
                      I have downloaded AmberTools12.tar.bz2 again. It
is downloaded in folder /home/sanjib/ Then I go to /home/sanjib .
Now the steps I followed:
$tar jxvf AmberTools12.tar.bz2
$cd amber12
$export AMBERHOME=/home/sanjib/amber12
$export http_proxy="http://sanjib:chemdyn11."
$./ --update-tree
(here bugfixes are downloaded. I wrote u what I got giving this
command in my previous mail)
$./configure gnu
bash: ./configure: No such file or directory

When I extract AmberTools.tar.bz2 these lines come at last portion.
bzip2: Compressed file ends unexpectedly;
        perhaps it is corrupted? *Possible* reason follows.
bzip2: Inappropriate ioctl for device
        Input file = (stdin), output file = (stdout)

It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.

You can use the `bzip2recover' program to attempt to recover
data from undamaged sections of corrupted files.

tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

If you need any further information please let me know. I will write u.


On 8/30/12, Jason Swails <> wrote:
> On Thu, Aug 30, 2012 at 12:33 PM, Sanjib Paul
> <>wrote:
>> Mr. Jason,
>> Thank you very much. I followed what you told. I set
>> environment variable http_proxy. Then give command
>> $./ --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
>> ,
>> $./configure gnu
>> bash: ./configure: No such file or directory
> This is a bad sign. Configure should be here, as long as you are in
>> I am giving what I got after command $./ --update-tree.
>> Please have a look.
>> and let me know what I am doing wrong.
>> $./ --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/
>> Creating file
>> /home/sanjib/amber12/AmberTools/src/parmed/ParmedTools/gui/
>> Creating file
>> /home/sanjib/amber12/AmberTools/src/parmed/chemistry/amber/
>> Creating file
>> /home/sanjib/amber12/AmberTools/src/parmed/chemistry/amber/
>> Creating file
>> /home/sanjib/amber12/AmberTools/src/parmed/chemistry/
> More bad news. 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 could not find them, but
> they should already exist. As a result, 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, 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
> _______________________________________________
> AMBER mailing list

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Received on Thu Aug 30 2012 - 12:00:04 PDT
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