Thank you James!
$ export AMBERHOME=/home/voronkov/amber11
$ export PATH=${AMBERHOME}/bin\:${PATH}
It works and maybe couple of comments regarding PATH specification, just couple of phrases in Amber may help, not only environment setup.
Best regards,
Andrew
04.11.2011, 22:31, "Ross Walker" <ross.rosswalker.co.uk>:
> 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
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>
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Received on Sun Nov 06 2011 - 07:30:03 PST
