On Mon, Dec 1, 2014 at 9:16 PM, Edward Kalkreuter <rekalkre.ncsu.edu> wrote:
> Hi,
>
> I am new to using Amber, so I am hoping it is a simple fix, but I have no
> idea what is going on at this point. I installed Ambertools14 on Ubuntu
> (with Virtualbox) following the instructions in the manual. I had no
> problems with this, and when I used the 'xleap' command, it worked great. I
> closed the program down though, and when I tried to use the 'xleap' command
> again, it said "xleap: command not found". I could not get it to work
> again, so I re-installed in the hopes that I missed a problem. The program
> worked great again after installing. I started doing the tutorials with
> good success; however, I shut my laptop off at the end of the day When I
> booted it up again tonight, I tried the commands 'sander' and 'xleap'.
> Neither one (or any other Ambertools command) is recognized (again,
> "command not found"). I can't install the program every time I want to use
> Amber, and I can't leave Ubuntu on the entire time either. Please let me
> know if you have suggestions.
>
You should specify what directions you are following. But what is
happening here is that during the course of the installation, it sets up
your environment variables (e.g., PATH and LD_LIBRARY_PATH) such that the
commands "xleap" and "sander" are in one of the directories that is
automatically searched for when looking for executables.
The instructions you are following *hopefully* tell you to source amber.sh
while installing -- and this is the command that sets up your environment
correctly. However, the command "source amber.sh" sets up your environment
ONLY for that shell session. As soon as you close your terminal, or open a
new one, or shut down, or whatever, the environment is reset to its
"default", and Amber is no longer a part of it. So you need to go to the
amber14 directory and run "source amber.sh" again... each time you start a
new terminal.
If you want this done automatically every time you start a terminal, you
need to make sure this command is in your .bashrc file. So if you
installed amber14 to your home directory, you should have a command like
the following in your ~/.bashrc file:
source ~/amber14/amber.sh
If you've done this and you are *still* getting the same behavior, then
your shell may not be automatically sourcing .bashrc on login. If that's
the case, you need to create a file called .bash_profile in your home
directory and put the following line in it:
test -f ~/.bashrc && source ~/.bashrc
This will make sure the environment is always properly loaded for Amber
when you open a shell. Close all shell windows and start a new one to make
sure the environment is properly set up in your new terminal window.
I would also suggest looking for a few UNIX command-line tutorials if you
are new to computational chemistry. The computer is our instrument, and
knowing how to use your instrument efficiently is critical to doing
effective research.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 01 2014 - 19:00:02 PST
