Hey Andrew!
For AmberTools 1.5 the directory you have to add to your PATH is
$AMBERHOME/bin and not $AMBERHOME/exe. I assume the bash is your shell.
The only thing required for you to do now is to set the AMBERHOME and
PATH environment variables properly. In your current shell, just type:
$ export AMBERHOME=/home/voronkov/amber11
$ export PATH=${AMBERHOME}/bin\:${PATH}
This defines AMBERHOME as you already had done, but then properly
prepends $AMBERHOME/bin to your PATH. You can make sure that this has
worked as expected by typing
$ which tleap
In your case this has to output `/home/voronkov/amber11/bin/tleap`. If
it prints nothing, your PATH is still not set correctly.
To make the environment changes permanent, add the export lines from
above to e.g. your ~/.bashrc file. If you would like to understand how
this mechanism works, you should read the "INVOCATION" part of the bash
manpage: http://linuxmanpages.com/man1/bash.1.php
Best regards,
Jan-Philip
On 11/04/2011 12:08 PM, Andrew Voronkov wrote:
> Dear Amber users, I have installed AmberTools version 1.5, but there are some problems with setup of the environment in basrc file because bash can't find the tleap. What might be the problem?
> The path is /home/voronkov/amber11/AmberTools
>
>
> Best regards,
> Andrew
>
> Installation of AmberTools, version 1.5 serial is complete at Fri Nov 4 13:55:15 MSK 2011.
>
> [voronkov.t60-2 src]$ tleap
> -bash: tleap: command not found
>
>
>
> AMBERHOME=/home/voronkov/amber11
> MPI_HOME=/opt/mpich-intel
>
> export AMBERHOME=/home/voronkov/amber11 # (for bash, zsh, ksh...)
> setenv AMBERHOME home/voronkov/amber11 # (for csh, tcsh)
> set path = ( $path $AMBERHOME/exe )
> PATH=$PATH:$AMBERHOME/exe
> export PATH
>
> # Source global definitions
> if [ -r /etc/bashrc ]; then
> . /etc/bashrc
> fi
>
>
> Best regards,
> Andrew
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Fri Nov 04 2011 - 05:00:03 PDT
