Just do the same as you have shown below, but instead of
gm.linux-rfml:/usr/local/newamber/amber12> cpptraj
you do
gm.linux-rfml:/usr/local/newamber/amber12> command -v cpptraj
From the output, you will see that the identified path to a cpptraj
executable is not the one you intended.
All you have to understand is that the directory containing the newest
cpptraj executable must be listed in your PATH environment variable
*before* any other directory containing an executable called cpptraj. At
any given time you can just look at your PATH variable via
$ echo $PATH
Probably your PATH environment variable contains multiple Amber bin
directories, whereas the one you actually want is not the first one.
That's why I wrote that you should *prepend* your $AMBERHOME/bin to PATH:
export AMBERHOME=/usr/local/newamber/amber12
export PATH=${AMBERHOME}/bin\:${PATH}
(Sorry Jason :-))
Right after that
gm.linux-rfml:/usr/local/newamber/amber12> command -v cpptraj
must show the path you expect.
In general, make sure that your ~/.bashrc file sets up a clean PATH
variable. Delete/outcomment PATH-modifying statements you think you
might not need anymore.
Cheers,
Jan-Philip
On 03/25/2013 02:16 PM, Vaibhav Dixit wrote:
> Hi, I made these changes to the .bashrc and sourced it, but cpptraj is
> still V12.1.
> Please suggest.
> gm.linux-rfml:~> cd $AMBERHOME
> gm.linux-rfml:/usr/local/newamber/amber12> vim /home/gm/.bashrc
> gm.linux-rfml:/usr/local/newamber/amber12> source /home/gm/.bashrc
> gm.linux-rfml:/usr/local/newamber/amber12> cpptraj
>
> CPPTRAJ: Trajectory Analysis. V12.1
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
>> quit
>
> gm.linux-rfml:/usr/local/newamber/amber12>
>
>
> export AMBERHOME=/usr/local/newamber/amber12
> export PATH=$PATH:$AMBERHOME/bin
>
>
> On Mon, Mar 25, 2013 at 4:51 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Mon, Mar 25, 2013 at 6:49 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
>>> wrote:
>>
>>> Dear Dr. Jan-Philip Gehrcke and amber people,
>>> They system is somehow not able to use new (right) executable.
>>> cd $AMBERHOME points to the right (newamber/amber12) directory.
>>> But the command you suggested strangely gives output about old
>> executable.
>>> And the creation dates/time for newamber/amber12/bin files are latest
>>> (today). I already have the following lines in my .bashrc which has been
>>> sourced.
>>>
>>> export PATH=$PATH\:$AMBERHOME/bin
>>> export AMBERHOME=/usr/local/newamber/amber12
>>> export PATH=$PATH:$AMBERHOME/exe
>>> export PATH=$USERPATH:$PATH
>>>
>>
>> You are appending AMBERHOME to the PATH before you even define AMBERHOME.
>> Then you proceed to add AMBERHOME/exe (which does not exist in Amber 12)
>> to the PATH afterwards. Change these lines of your bashrc to 2 simple
>> ones:
>>
>> export AMBERHOME=/usr/local/newamber/amber12
>> export PATH=$PATH:$AMBERHOME/bin
>>
>> As Jan-Philip mentioned, USERPATH is unrelated to Amber, so whatever you do
>> with that variable is up to you.
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Mon Mar 25 2013 - 07:00:02 PDT
