Re: AMBER: installation

From: Mark Williamson <>
Date: Sat, 29 Dec 2007 17:23:15 +0000

s lal badshah wrote:

> ahmad.uop:~/amber9> #tar xvzf amber9.tgz
> ahmad.uop:~/amber9> #cd amber9
> ahmad.uop:~/amber9> #make
> ahmad.uop:~/amber9> #make install
> ahmad.uop:~/amber9> export AMBERHOME="/usr/local/amber9_mpich"
> ahmad.uop:~/amber9> export MPICH_HOME="/usr/local/mpich-"
> ahmad.uop:~/amber9> cd $AMBERHOME/src
> bash: cd: /usr/local/amber9_mpich/src: No such file or directory
> ahmad.uop:~/amber9> ./configure ifort
> bash: ./configure: No such file or directory
> ahmad.uop:~/amber9> make serial
> bash: make: command not found

These comments are in addition to Ross' advice already presented in this

I think the majority of your problems stem from a mistake at the very
beginning. If you have typed these commands exactly as stated in your
email and you're using BASH (I'm assuming this since the export command
is functioning here, albeit with an undesired effect), then the first
four commands will not actually have been executed since they are
prefixed with the "#" symbol. Within BASH, this a comment symbol, hence
the shell will not carry out any commands on a line that starts with
this symbol. Therefore, you will need to execute the first four commands
above without the "#" symbol.

A second point, the commands in lines 3 and 4 are not needed. I'm not
sure why you are using them at this point here.

Thirdly, given the tar command in line 1 and given that you started the
above sequence of commands in the /usr/local/ directory, (as Ross says),
your AMBERHOME environment variable should be /usr/local/amber9 and not
/usr/local/amber9_mpich . But I suspect from the command line prompt
that you're actually in the /home/ahmad/amber9 directory, hence
AMBERHOME should be /home/ahmad/amber9/amber9 . You need to check this.

Given the above, it suggests that your grasp of the unix command line
may need improving; it may be useful reading up on some command line
basics. This might be useful; . Don't be
afraid to google for some more; there's a lot of good ones out there.


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Received on Sun Dec 30 2007 - 06:07:33 PST
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