On Wed, Jun 01, 2016, Angelina Malagodi wrote:
Let me try to expand on what Hai wrote, just to have best chance of solving
your problem.
> My installation process goes through these commands each time:
>
> tar jxvf AmberTools15.tar.bz2
> tar jxvf Amber14.tar.bz2
> cd amber14
> export AMBERHOME=`pwd`
> ./configure gnu
> source amber.sh
> make install
> echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
1. What directory did you start from? Use "echo $AMBERHOME" to find
out what AMBERHOME is really set to.
2. What you describe above should work. But your descriptions suggest that
maybe somehow you didn't really do this.
> > Yes, ran the source command (MacBook-Pro:~ XX$ source $AMBERHOME/amber.sh
> > -bash: /amber.sh: No such file or directory)
The message from bash indcates that "$AMBERHOME/amber.sh" was expanded to
"/amber.sh", i.e. that your AMBERHOME variable was not set (i.e. was empty).
> However, if I do MacBook-Pro:~ XX$ vim .bashrc, it indicates that source
> /Applications/amber16/amber.sh
The above suggests that you began your installation in the /Applications
directory, which is possible but odd. The final line of your .bashrc
should say "source <actual-value-of-AMBERHOME-here>/amber.sh". If you did
start from /Applications, is it possible that you got mixed up between
"amber14" and "amber16"? Navigate to your $AMBERHOME directory, and see which
subdirectories are there.
In any event, don't reinstall Amber each time!
...good luck....dac
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Received on Wed Jun 01 2016 - 17:30:02 PDT
