Dear Daniel
Thanks for your quick reply.
I obtained AmberTools14.tar.bz2 from
http://ambermd.org/AmberTools14-get.html.
The size of downloaded AmberTools14.tar.bz2 is 1748632.
I downloaded it again. Unfortunately, the size is the same.
Is there alternative way to obtain AmberTools14.tar.bz2?
What is md5sum? There is only AmberTools14 in above link.
Is md5sum mandatory for installation?
Best wishes,
Atila
On Sun, Jan 18, 2015 at 10:08 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The size of AmberTools14.tar.bz2 should be 212395464, and the md5sum
> should be 589cc9bd17b15ce3f9604b0bdeea3bab. If not, your download may
> have been truncated or otherwise corrupted somehow and you should try
> downloading the file again.
>
> Hope this helps,
>
> -Dan
>
> On Sun, Jan 18, 2015 at 11:22 AM, Atila Petrosian
> <atila.petrosian.gmail.com> wrote:
> > Dear amber users
> >
> >
> >
> > I have an mdcrd file obtained from amber 10. Now I don’t have AMBER and
> > only I want to do some analysis using cpptraj in AmberTools14. Thus, I
> want
> > to install AmberTools14 on Ubuntu.
> >
> > Based on the chapter 2 of the Amber14 Reference Manual
> > <http://ambermd.org/doc12/Amber14.pdf>, I have done following steps:
> >
> > 1) export AMBERHOME=/home/myname/amber14
> >
> > 2) sudo apt-get install build-essential gfortran libbz2-dev libz-dev
> > xorg-dev
> >
> > 3) tar -jxf AmberTools14.tar.bz2
> >
> > During untarring, I encountered with
> >
> > 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
> >
> > Then, I used bzip2recover AmberTools14.tar.bz2
> >
> > 4) cd $AMBERHOME
> >
> > 5) ./configure gnu
> >
> > Checking for updates...
> >
> > Checking for available patches online. This may take a few seconds...
> >
> >
> >
> > I have a question. In earlier versions, I should use bugfixes. Isn’t it
> > necessary to use bugfixes in AmberTools14?
> >
> > Is my installation manner true?
> >
> >
> > Any help will highly appreciated.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 18 2015 - 11:30:02 PST
