Re: [AMBER] No exe file in Amberhome

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 24 Feb 2016 12:24:54 -0500

Also note that LD_LIBRARY_PATH is for Linux only. This won't work on macs (and the Abort Trap error is one I usually see associated with macs).

It's better to *just* source amber.sh (or amber.csh). It sets all of the environment variables that AMBER needs.

HTH,
Jason 

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
> On Feb 23, 2016, at 12:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 
> 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
>>> 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
> 
> 
> 
> -- 
> -------------------------
> 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)
> 
> _______________________________________________
> 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
Received on Wed Feb 24 2016 - 09:30:05 PST
Custom Search