Re: [AMBER] PATH/evironment problem on Mac OS X

From: Ben Roberts <>
Date: Fri, 21 Jan 2011 13:00:50 -0500

Hi Gustav,

On 21/1/2011, at 12:46 p.m., Gustaf Olsson wrote:

> Thank you Jason!
> I should have been a bit more detailed with my question.
>> Small comment here: use bin rather than exe, since the use of exe is being phased out.
> Usually I use /bin. I just tried /exe to see if it made a difference, forgot to change back.
>> No. AMBERHOME and PATH are different environment variables. Put the following in your .profile or .bashrc:
>> export AMBERHOME=/usr/local/amber11
>> export PATH=$AMBERHOME/bin:$PATH
>> and retry.
> This is what I have in my .profile and have also tried in .bashrc as well as global profile and bashrc
> export AMBERHOME=/usr/local/amber11
> export PATH=${AMBERHOME}/bin:$PATH
> Tried the suggestion without {}, but it did not make a difference!
> I just don't understand, I've tried exporting in all profiles on the mac and nothing solves this problem. I might also add that we've compiled AmberTools successfully in three iMac:s running Snow Leopard, and they all break during the "tests" with the same error.
> Anything else anyone suggests I should try before starting to dissect the code?

In your bashrc or bash_profile or wherever, try echoing $AMBERHOME and $PATH (with the dollar signs in this case) just after you've set them. It may be that some other resource file you're loading is messing your environment up.

Also, run "env | grep PATH" and "env | grep AMBERHOME" just before you might run the tests, and see what you can see.


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Received on Fri Jan 21 2011 - 10:30:04 PST
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