AMBER Archive (2006)

Subject: Re: AMBER: Installing / Compiling Question

From: David A. Case (case_at_scripps.edu)
Date: Sat May 27 2006 - 23:50:54 CDT

On Sat, May 27, 2006, Seth Lilavivat wrote:
>
> What is the proper
> way to define all of the environment variables in a bash shell? I editted
> the .bash_profile and followed what the Amber manual but said to do but the
> result wasn't always what I expected. For example:
>
> set AMBERHOME=/usr/local/amber8
> export AMBERHOME

The first line is an error in the manual; remove the "set" from that line.
>
> Did not seem to have any affect, the following seems to work ok.
>
> export AMBERHOME="/usr/local/amber8"

This is generally how it would work; the two-command version is required
on some older versions of the Bourne shell.

> Another thing I find baffling is why I still get a "Command not found" error
> even when I am in the directory that I am typing the particular executable.

You need to have "." in your PATH variable -- it is not there by default,
as it would be on windows, for example.

> I also would like to know how to properly add $AMBERHOME/exe to my PATH.

Try something like this:

    export PATH=".:$AMBERHOME/exe:$PATH"

This will add the current directory, plus $AMBERHOME/exe to whatever is
already in your PATH variable. (Try "echo $PATH" before and after the above
command.)

...good luck...dac

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