Hi Filip,
This is confusing. The section of the bash script this is referring to is
really simple:
tar -xjf $1 amber11/amber_bugfix_1_to_16.txt
if [ $? -ne 0 ]; then
echo "Error extracting amber_bugfix_1_to_16.txt from archive!"
echo "Corrupt archive. Download patch bugfix.1to17.tar.bz2 again and
re-apply"
exit 1
fi
Where $1 is whatever you gave as the first command line argument to the
apply_patch.x script.
So, assuming you saved the bugfix file in the current working directory
then:
apply_bugfix.x bugfix.1to17.tar.bz2
should work fine. Check that the path you are giving to the bugfix tar file
is correct. Check with 'ls -la' to make sure it is in the directory you are
running the apply_bugfix.x file from and that it does not have zero bytes
size. The file is large so could take a while to download. Some browsers etc
create temporary files until the download is complete or insist on putting
everything in a central 'Downloads' directory so this could be your problem.
All the best
Ross
> -----Original Message-----
> From: filip fratev [mailto:filipfratev.yahoo.com]
> Sent: Friday, August 19, 2011 10:21 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber 11 bugfix/Cuda update
>
> I have the same problem with the new patch:
> tar (child): bugfix.1to17.tar.bz2: NO such file....
> tar (child): Error is not recoverable: exiting now
> tar: Child returned status 2
> tar: Error is not recoverable: exiting now
> Error extracting amber_bugfix_1_to_16.txt from archive!
> Corrupt archive. Download patch bugfix.1to17.tar.bz2 again and re-apply
>
> Regards,
> Filip
>
>
>
>
>
>
> ----- Original Message -----
> From: Jason Swails <jason.swails.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Cc:
> Sent: Friday, August 19, 2011 6:04 PM
> Subject: Re: [AMBER] Amber 11 bugfix
>
> You need to supply the path of the bugfix.1to17.tar.bz2 for
> apply_bugfix.x
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Aug 19, 2011, at 10:54 AM, "Jennifer L. Muzyka"
> <jennifer.muzyka.centre.edu> wrote:
>
> > When I type echo $AMBERHOME, I get
> /Users/jennifer.muzyka/opt/amber11. I have downloaded the script and
> the patch tarball both to the same amber11 directory.
> > Jennifer
> >
> >
> > On Aug 19, 2011, at 10:51 AM, David A Case wrote:
> >
> >> On Fri, Aug 19, 2011, Jennifer L. Muzyka wrote:
> >>
> >>> I'm trying to install the Amber 11 bugfixes before installing
> >>> Amber 11. When I try to apply the bugfix patch as described
> >>> at ambermd.org/bugfixes11.html (using ./apply_bugfix.x
> >>> bugfix.1to17.tar.bz2), I get the following error:
> >>> tar: Error opening archive: Failed to open
> 'bugfix.1to17.tar.bz2': No
> >>> such file or directory
> >>
> >> I'm guessing this arises because your AMBERHOME environment variable
> is not
> >> set correctly. It should point to the amber11 tree. Can you see if
> that is
> >> the problem?
> >>
> >> ...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > Jennifer L. Muzyka
> > Professor of Chemistry
> > Centre College
> > 600 West Walnut Street
> > Danville, KY 40422
> >
> > jennifer.muzyka.centre.edu
> > http://web.centre.edu/muzyka/
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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Received on Fri Aug 19 2011 - 10:30:07 PDT
