We talked in the UNIX manual about
these silly variable types that start with $, like $AMBERHOME.
But what happens when there isn’t actually an $AMBERHOME?
$ $AMBERHOME/bin/cpptraj
-bash: /bin/cpptraj: No such file or directory
Check your ~/.bashrc file.
The following two lines need to appear in your ~/.bashrc file
(with the correct version of AMBER referenced (16, 18, etc.), and sourcing
amber.csh if you’re using a c-shell environment).
export AMBERHOME="/usr/local/amber18"
source "$AMBERHOME/amber.sh"
If they’re not there, then you need to add them with either
vi or gedit.
After adding them, make sure you use $ source ~/.bashrc to actually make
them available.