Thank you
Its clear now :)
James
2011/11/4 Jan-Philip Gehrcke <jgehrcke.googlemail.com>
> Hey James, see comments below.
>
> On 11/04/2011 01:52 PM, James Starlight wrote:
> > Jan-Philip, hello!
> >
> > I have the same problem
> >
> > But there are four different .bashrc
> >
> > own.owntest:~/Desktop$ locate .bashrc
> > /etc/bash.bashrc
> This file belongs to root and is responsible for system wide
> configuration. If you don't want to set AMBERHOME and corresponding PATH
> for all users on this host, then don't edit this file.
>
> > /etc/skel/.bashrc
> This one not, either. It's the default configuration for new users.
>
> > /home/own/.bashrc
> This is the one you want to edit (assuming that you are working as the
> "own" user).
>
> > /usr/share/base-files/dot.bashrc
> I don't know what this file is exactly good for. I think it's some
> default system wide config. You for sure don't want to edit it.
>
> > /usr/share/doc/adduser/examples/adduser.local.conf.examples/bash.bashrc
> >
> /usr/share/doc/adduser/examples/adduser.local.conf.examples/skel/dot.bashrc
> Those ones are for documentation...
>
>
> >
> > which exactly .barhrs I should to modify?
> >
> > JAmes
> >
> >
> > 2011/11/4 Jan-Philip Gehrcke<jgehrcke.googlemail.com>
> >
> >> 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Nov 04 2011 - 07:00:03 PDT
