Hi James and Other AMBER Users,
I think it is our opinion as developers, and others can chime in here, that
one should NOT add $AMBERHOME/bin to the path. This can be dangerous since
we don't choose executable names to be unique etc. Thus you could
accidentally run the wrong command by mistake. It also means you might be
running an older version of the code without realizing it if you don’t check
what's in the path. A similar problem occurs with Gaussian that uses the
name 'gv' for Gaussview that clashes with ghostview for example.
My suggestion would be that ALL amber command should be run with the
$AMBERHOME/bin prefix. That is you would do:
$AMBERHOME/bin/xleap
...
$AMBERHOME/bin/pmemd.cuda
etc. That way if you echo $AMBERHOME before you start you won't get any
surprises later about running the wrong version by mistake etc. I think this
is good discipline to have when doing scientific research.
All the best
Ross
> -----Original Message-----
> From: James Starlight [mailto:jmsstarlight.gmail.com]
> Sent: Friday, November 04, 2011 6:48 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] bashrc problems
>
> Thank you
> Its clear now :)
>
> James
>
> 2011/11/4 Jan-Philip Gehrcke <jgehrcke.googlemail.com>
>
> > Hey James, see comments below.
> >
> > On 11/04/2011 01:52 PM, James Starlight wrote:
> > > Jan-Philip, hello!
> > >
> > > I have the same problem
> > >
> > > But there are four different .bashrc
> > >
> > > own.owntest:~/Desktop$ 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.ba
> shrc
> > 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Nov 04 2011 - 12:00:06 PDT
