Yes, sorry I forgot that part. When making changes to /etc/profile or ~/.bashrc you either have to log out and back in or *source* them.

Really thankful for you help!
Yes it can be run now.
Thousands of thanks

You're most welcome. Glad it's working

uh oh..
just found out that the commands other than clustalw will not work again..
ls, cd and all.
Then i did a
export PATH=$PATH:/bin:
ls, cd and some commands worked.
But not whereis, rmmod, cluster-fork.

Anymore suggestions?
These paths are going to drive me crazy..

I think you may need to take a step back and spend a few minutes looking at a larger picture so you don't get lost in details.
Think for a moment about what your $PATH is. I may say some things here that are obvious, but it may help.

$PATH is a variable which lists a string of directories that applications search for executable files. Using these directories allows you and your scripts to call applications without the need for an exact path to these commands. It's kinda like saying "I'm going to Sam's house"...you don't need to say "I'm going to Sam's house at 15 Rogers Street, Chicago, Illinois" because the path to his house is already known.

There are a few files which set what directories are in $PATH. /etc/profile and/or /etc/bashrc set a global $PATH, and $HOME/.bashrc sets the $PATH for individual users.
With $HOME/.bashrc you can either append directories to the global $PATH or you can completely replace it with your own $PATH. If you want to append, you must include "$PATH" in the value of your new $PATH: PATH=$PATH:~/bin:/opt/firebird:~/scripts
If you do not include the original $PATH, your new path will consist of only the directories listed in $HOME/.bashrc, and the global $PATH will be ignored.

The global $PATH is usually already set with the essential system binary directories such as /bin and /usr/bin. If you find that a lot of standard commands don't work anymore, chances are you either removed the paths from the global $PATH or you replaced the global $PATH completely (failed to include "$PATH" in your local $PATH).

First thing I'd do is check the global settings, located in /etc/profile or perhaps a bash configuation file such as /etc/bashrc or /etc/bash.bashrc. This should show you all the standards:
/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin...if all of these (and perhaps a few more) are not set in /etc/profile, you're likely to have trouble.

What I like to do is LEAVE GLOBAL FILES ALONE as much as possible, and use only local configuration files whenever I can. Setting a $PATH locally to me means appending only...I leave the $PATH in /etc/profile as it is and add directories to it in $HOME/.bashrc, as mentioned above.

As an added note, your $PATH may be altered by other scripts beyond /etc/profile and $HOME/.bashrc. It's possible that you have afaulty script somewhere that completely replaces $PATH instead of appending to it.

I hope this helps a little.

Thanks milkshaw.
My echo $PATH show
/opt/BioBrew/ClustalW/1.8.3/bin:/usr/local/sbin:/opt/BioBrew/ClustalW/1.8.3/bin:/usr/local/sbin:/opt/BioBrew/ClustalW/1.8.3/bin:/bin::/usr/X11R6/bin:/opt/ganglia/bin:/opt/maui/bin:/
And a lot of repeated paths..

When i tried to source /etc/profile:
bash: id: commad not found
[: =: unary operator expeeted
bash: id: command not found
bash: dircolors: command not found.

But in my /etc/profile i only have:
export PATH=/opt/BioBrew/ClustalW/1.8.3/bin:/usr/local/sbin:/sbin:$PATH
Where did the extra lines come from?

Somehow it works again.
Thanks for all the help!