Hi Jan-Philip,
Thanks for the reply. Now with the following settings:
export AMBERHOME=/home/user/amber11
export PATH=$PATH:/home/user/amber11/bin:/directory on cluster for
amber/amber11/bin
`which MMPBSA` returns /home/user/amber11/bin/MMPBSA
`which sander` returns /directory on cluster for amber/amber11/bin/sander
So there are all right now. But when running decomposed MMPBSA
calculations, "Error: sander could not be found!" still exists. So it seems
that the program can only search executables in $AMBERHOME/bin.
How to do it in Ambertools1.5 for the program to find executables in the
full PATH when they can't be found in $AMBERHOME/bin?
In Ambertools12, there is a variable ‘search_path’ in the input file to
control this. But how about in Ambertools1.5 please? Thanks for any advice.
Qiong
On Tue, May 22, 2012 at 11:21 AM, Jan-Philip Gehrcke <
jgehrcke.googlemail.com> wrote:
> Hello Qiong,
>
> if `which MMPBSA` finds the wrong executable, the order of directories
> still is wrong in your PATH environment variable. Make sure that your
> new AMBERHOME directory appears in $PATH before any other Amber-related
> directories. By doing so, your shell will find and use the MMPBSA
> executable in your new AMBERHOME directory.
>
> You accomplish that via e.g.
>
> export AMBERHOME=/home/user/amber11
> export PATH=${AMBERHOME}/bin\:${PATH}
>
> This *prepends* your AMBERHOME/bin directory to your PATH.
>
> You have to make sure by yourself that after executing these lines no
> other script is prepending a 'wrong' directory to the PATH. In any case,
> if you still have problems, you should validate the order of directory
> occurrences in PATH manually:
>
> echo $PATH
>
> Hope this helps,
>
> Jan-Philip
>
>
>
> On 05/22/2012 04:59 PM, Qiong Zhang wrote:
> > export AMBERHOME=/home/user/amber11
> > export PATH=$PATH:$AMBERHOME/bin:/directory on cluster for
> amber/amber11/bin
>
>
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Received on Tue May 22 2012 - 09:00:05 PDT
