AMBER: Installing / Compiling Question

From: Seth Lilavivat <>
Date: Sat, 27 May 2006 04:29:06 +0100

Dear All,

when doing a "make install" on leap, I get the following message:

/usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.a when searching for
/usr/bin/ld: cannot find -lXt
collect2: ld returned 1 exit status
make[1]: *** [xaLeap] Error 1
make[1]: Leaving directory `/usr/local/amber8/src/leap/src/leap

After searching the mail archives, it was suggested that this had to do with
the face that the environment variables have not been set properly... in
which case leads me to an even more important question. 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

Did not seem to have any affect, the following seems to work ok.

        export AMBERHOME="/usr/local/amber8"

What is unusual is that when deleting these lines from my .bash_profile,
exiting the bash shell and opening a new one, I am still able to do the

        cd $AMBERHOME

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.
I also would like to know how to properly add $AMBERHOME/exe to my PATH.
Obviously I'm not understanding the what is going on when setting my
environment and I've googled so many Linux bash tutorials that my head is
spinning. Please help.

Seth Lilavivat
Georgia Institute of Technology

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Received on Sun May 28 2006 - 06:07:07 PDT
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