Hi
After the start of these questions I followed and managed to install
AmberTools15 properly and could also solve other problems with files
in python MCPB.py and parmed.py that had no libraries and the way which
indicated python look, below overview:
...Hi
I had a similar problem in python2.7 respectively scripts for
MCPB.py and parmed.py
managed to solve AmberTools15 reinstalling as follows:
First installed libraries missing:
http://www.scipy.org/install.html
sudo apt-get install python-numpy python-scipy python-matplotlib ipython
ipython-notebook python-pandas python-SymPy python-nose
do this before installing
tar jxvf Amber15.tar.bz2
export AMBERHOME=`pwd`
./configure --with-python /usr/bin/python2.7
source amber.sh
make install
make test
The following command to install in parallel (requires first install mpi
with the same compiler gnu)
./configure --with-python /usr/bin/python2.7 -mpi gnu
make install
then it was just to set the bash file contents amber.sh
In my case:
export AMBERHOME="/home/marcelo/PROGRAMS/AMBER-NEW/amber14"
export PATH="${AMBERHOME}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages"
else
export
PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
fi
The problem in my case it was because they lacked python files and to set
needed which seek python2.7
...
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 14:05 GMT-03:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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
>
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Received on Wed Feb 24 2016 - 04:00:05 PST
