Ok. I understand it! after exporting, I should use this
source $AMBERHOME/amber.sh
To source amber.sh, then I could use other commands.
True?
________________________________________
From: Mahdieh Hadi [mahdieh.hadi.bric.ku.dk]
Sent: Wednesday, February 24, 2016 11:13 AM
To: AMBER Mailing List
Subject: Re: [AMBER] No exe file in Amberhome
So, should I use just the following commands to install amber?
tar jxvf AmberTools15.tar.bz2
tar jxvf Amber14.tar.bz2
cd amber14
export AMBERHOME=`pwd`
./configure gnu
# We recommend you say "yes" when asked to apply updates
source amber.sh # Use amber.csh if you use tcsh or csh
make install
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc # Add Amber to your environment
and whenever I restart, shutdown, etc,
I should use
Export AMBERHOME= /Users/Amber14
Is it true?
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, February 23, 2016 6:05 PM
To: AMBER Mailing List
Subject: Re: [AMBER] No exe file in Amberhome
Hi,
On Tue, Feb 23, 2016 at 9:44 AM, Marcelo Andrade Chagas
<andrade.mchagas.gmail.com> wrote:
> PATH = $ PATH: $ HOME / PROGRAMS / amber14 / bin :.
>
> export PATH
> # Setting PATH
> export AMBER14 AMBERHOME = "/ home / Marcelo / PROGRAMS / amber14"
>
> export LD_LIBRARY_PATH = "$ {AMBERHOME} / lib"
>
> export LD_LIBRARY_PATH = "$ {LD_LIBRARY_PATH}: $ {AMBERHOME} / lib"
You are trying to setup your environment manually, which you really
shouldn't need to do after sourcing 'amber.sh'. In fact it seems that
you overwriting your LD_LIBRARY_PATH so that it only contains
'$AMBERHOME/lib', which will probably break how things work on your
system (I'm assuming you don't really have those spaces in there since
bash would complain otherwise). Just sourcing 'amber.sh' should be
enough to get Amber to work properly.
-Dan
>
> Best regards
>
> Marcelo
>
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2016-02-23 10:25 GMT-03:00 Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>:
>
>> Hi again,
>> I have run the following code to test the amber installation,
>>
>> Cd Users
>> tar xvfj AmberTools15.tar.bz2 # (Note: extracts in an # “amber14”
>> directory)
>> export AMBERHOME=/Users/amber14 # (for bash, zsh, ksh, etc.)
>> cd $AMBERHOME
>> ./configure –help
>> ./configure gnu
>> source /users/amber14/amber.sh # for bash, zsh, ksh, etc.
>> make install
>> make test
>>
>> and it seems that there are no errors!
>> The final sentences of the test code are as follows:
>>
>>
>> Installation of AmberTools14 serial is complete at Tue Feb 23 14:23:54 CET
>> 2016.
>>
>> ==============================================================
>> /Users/amber14/src/Makefile not found, or -noamber was set.
>> This is expected if you do not have Amber14.
>> ==============================================================
>> MHA:amber14 mha$ make test
>>
>> I don't know what could be the reason behind the past mentioned error :(
>>
>>
>> ________________________________________
>> From: David A Case [david.case.rutgers.edu]
>> Sent: Tuesday, February 23, 2016 1:52 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] No exe file in Amberhome
>>
>> On Tue, Feb 23, 2016, Mahdieh Hadi wrote:
>> >
>> > dyld: Library not loaded: /Users/mha/amber14/lib/libfftw3.3.dylib
>> > Referenced from: /Users/amber14/./a.out
>> > Reason: image not found
>> > Trace/BPT trap: 5
>>
>> This looks like a problem with the AmberTools installation. I'd suggest
>> that
>> you re-configure and compile, and look carefully for errors related to
>> fftw3.
>>
>> Also, be sure to run the test cases: given the problem above, it seems
>> likely
>> that all the nab-based test cases will fail. It makes a big difference in
>> the
>> sorts of advice we give if we know whether you have a working AmberTools
>> installation or not.
>>
>> ....good luck....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 24 2016 - 02:30:06 PST
