Re: [AMBER] Error in making and running xleap

From: Jason Swails <>
Date: Thu, 28 Aug 2014 07:34:59 -0400

On Thu, 2014-08-28 at 14:52 +0500, wrote:
> Hello
> I downloaded a new copy of AmberTools14 from
> "". But when I tried to extract the
> downloaded folder named "AmberTools14.tar.bz2" by using command "tar
> xvf AmberTools14.tar.bz2" it gave the following error
> 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.
> The partially extracted folder does not have "dat" directory in it :(

My guess is that the download did not finish. To check that the file is
"correct" (i.e., that it is the same file with all of the same bytes as
the one that I have), check its exact size and md5sum. Here are the
results I get on my computer (which exactly match the values you are
told they should be on

swails.batman /usr/local $ ls -l AmberTools14.tar.bz2
-rw-r--r-- 1 swails swails 212395464 Apr 17 12:34 AmberTools14.tar.bz2

swails.batman /usr/local $ md5sum AmberTools14.tar.bz2
589cc9bd17b15ce3f9604b0bdeea3bab AmberTools14.tar.bz2

So the tarball should be 212395464 bytes (203 MB) large with the md5sum
shown above. If it's not, something went wrong with the download, and
you should try again. Until your downloaded file matches the statistics
above, it will not work.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Aug 28 2014 - 05:00:02 PDT
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