On Sat, Dec 19, 2009 at 6:59 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi All,
>
> I am trying to install the release candidate of AMBER Tools and followed the
> instructions in amber11/Readme_at in the release. There appear to be some
> minor problems:
>
>
> Quick installation instructions:
>
> 1. Set your AMBERHOME environment variable, e.g.
>
> export AMBERHOME=/usr/local/amber11 (for bash, zsh, ksh...)
> setenv AMBERHOME /usr/local/amber11 (for csh, tcsh)
>
> Note: be sure to change the "/usr/local" above to what it should
> be for your machine. Also, you should add $AMBERHOME/bin to your
> $PATH.
Wouldn't it make more sense to set AMBERHOME after the tar file has
been extracted? Extracting this file creates the amber11 directory
> 2 Uncompress the tar file:
>
> cd $AMBERHOME/..
> tar xvfj AmberTools-1.3.tar.bz2
If you do this, AMBERHOME would become $AMBERHOME/amber11, so it would
have to be updated, right? Or am I missing something...
>
> Consider I am in my home directory and I download and save the .tar.bz2 file
> here. I then do:
>
> export AMBERHOME=/scratch/amber11
>
> Then
>
> cd $AMBERHOME/..
>
> this returns:
>
> -bash: cd: /scratch1/amber11/..: No such file or directory
>
> And I end up still in my home directory. The tar extraction then extracts
> AmberTools-1.3 into ~/amber11.
>
> I think it would make more sense if this read.
>
> 2 Uncompress the tar file:
>
> mkdir $AMBERHOME
> cd $AMBERHOME/..
> tar xvjf /path_to/AmberTools-1.3.tar.bz2
Perhaps: tar xvjf /path/to/AmberTools-1.3.tar (it should already be
uncompressed)
cd amber11
export AMBERHOME=`pwd` -or-
setenv AMBERHOME `pwd` for tcsh/csh
(In fact, this is not terribly important for install, since the
configure script overrides this anyway, but it's important later on)
>
> Of course the README_at file is inside the tar.bz2 file so this is kind of a
> chicken and egg problem anyway.
Agreed, though isn't it available on the web? In which case I suppose
there's an argument that the egg came first ;-).
> 3. Change directory to src. Type "./configure -help" and choose
> options for your computer. Then configure:
>
> ./configure gnu (example: should work for most systems)
>
> This should be:
>
> 3. Change directory to $AMBERHOME/src. Type "./configure -help" and choose
> options for your computer. Then configure:
>
> cd $AMBERHOME/src
> ./configure gnu (example: should work for most systems)
>
>
> Comments? Shall I just update the Readme in amber11 cvs tree and the at1.3
> branch?
Those are my 2 cents.
Thanks!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Sat Dec 19 2009 - 08:00:03 PST
