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
>>
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Received on Fri Nov 04 2011 - 06:30:03 PDT
