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Mod:Hunt Research Group/Jan install

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Installing Jan's Charge Analysis Code

python

  • you will need python3.5
  • and python packages matplotlib, scipy and fortranformat
  • see the group python wiki pages for instructions

RESP

  • this is a free program to perform ESP-fitting,
  • goto the webpage "http://upjv.q4md-forcefieldtools.org/RED/resp/"
  • scroll to the bottom and download the standalone version 2.2
  • read the README file
  • copy standalone-resp-2.2.tgz into your /tricia/bin directory,
  • double click to gunzip and untar or do this manually "tar -zxvf standalone-resp-2.2.tgz"
  • then cd tricia/bin/resp-2.2 and check the Makefile has FC=gfortran
  • then type make ie "/Users/tricia/bin/resp-2.2 $ make"
  • you should now see a file resp.o and resp.f
  • you will need access to this in your your PATH variable
  • in your .bashrc file add "export PATH=$PATH:/Users/$USER/bin:" if it is not there already

you will need X11

AmberTools

the instructions for High-Sierra are below

  • goto "http://ambermd.org/GetAmber.php"
  • goto "http://ambermd.org/Installation.php"
  • expand the downloaded file, this can take a while be patient.
  • you will get a directory amber16 re-name this to amber17
  • edit the .bashrc to add "export AMBERHOME="/Users/tricia/bin/amber17" and re-execute ". .bashrc"
  • edit the .login to add "setenv AMBERHOME /Users/tricia/bin/amber16" then re-execute the login in c-shell:
csh
source .login
exit
  • now to set up the configure file
gcc49 is not available on High Sierra (was used pre High Sierra)
we will use the clang compilers for gcc and gfortran and we will activate the -macAccelerate flag
cd $AMBERHOME
./configure --help
./configure -macAccelerate clang
  • it will ask if you want to install miniconda, accept
  • now we will install it, type
make install
make test
this will take some time!
  • hopefully it will work … we have had problems!
  • you should see something like this
"installation of AmberTools16 serial is complete at Wed 24 Aug 2016 12:43:26 BST."
  • don’t worry if you also see this as we only want amber tools and is expected if you do not have Amber16.
"/Users/tricia/bin/amber16/src/Makefile not found, or -noamber was set."

the instructions for pre High-Sierra are below

  • goto "http://ambermd.org/AmberTools16-get.html" pre High-Sierra
  • the Safari download did not work so use Firefox for this, fill in your information to start the download
  • expand the downloaded file, this can take a while be patient.
  • you will get a directory amber16
  • read the README file and goto the installation documentation and follow the instructions
  • also for MacOX you will need to visit this page "http://jswails.wikidot.com/installing-amber12-and-ambertools-13"
  • edit the .bashrc to add "export AMBERHOME=/Users/tricia/bin/amber16" and re-execute ". .bashrc"
  • edit the .login to add "setenv AMBERHOME /Users/tricia/bin/amber16" then re-execute the login in c-shell:
csh
source .login
exit
  • to instal amber16 we will need to install the following using MacPorts
the problem is this needs old python (2.7.12) not new python (3.5)
and we need specific gcc compilers
sudo port install gcc49
sudo port install mpich-gcc49
sudo port select --set gcc mp-gcc49
sudo port select --set mpi mpich-gcc49-fortran
sudo select -- list python
sudo port select --set python python27
sudo port install py35-readline
sudo port install py27-matplotlib
sudo port install py27-scipy
sudo port install py27-numpy
sudo port install py27-tkinter
  • now back to the amber installation instructions, use the configure help
we will use the gnu compilers gcc and gfortran and we will activate the -macAccelerate flag
cd $AMBERHOME
./configure --help
./configure -macAccelerate gnu

•as it compiles check it is using the right version of python, you should see printed

“Compatible Python found! Using /opt/local/bin/python”

•when this completes execute "source amber.sh" and add the contents of "amber.sh" to your .bashrc file 

#
# amber and ambertools is needed for repESP to work
#
  export AMBERHOME=/Users/tricia/bin/amber16
  export PATH="$PATH:${AMBERHOME}/bin"
if [ -z "$PYTHONPATH" ]; then
    export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages"
else
    export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
#
  • now we instal, this this will take some time!
make install
make test
  • hopefully it will work … we have had problems!
  • you should see something like this
"installation of AmberTools16 serial is complete at Wed 24 Aug 2016 12:43:26 BST."
  • don’t worry if you also see this as we only want amber tools and is expected if you do not have Amber16.
"/Users/tricia/bin/amber16/src/Makefile not found, or -noamber was set."

repESP code

python3.5 setup.py develop
  • you should see something like the following (which is not complete)
running install
running bdist_egg
running egg_info
creating repESP.egg-info
writing requirements to repESP.egg-info/requires.txt
writing dependency_links to repESP.egg-info/dependency_links.txt
writing top-level names to repESP.egg-info/top_level.txt
writing repESP.egg-info/PKG-INFO
writing manifest file 'repESP.egg-info/SOURCES.txt'
reading manifest file 'repESP.egg-info/SOURCES.txt'
writing manifest file 'repESP.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.6-intel/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/repESP
copying repESP/__init__.py -> build/lib/repESP
copying repESP/charges.py -> build/lib/repESP
copying repESP/cube_helpers.py -> build/lib/repESP
copying repESP/esp_fit_calc.py -> build/lib/repESP
copying repESP/field_comparison.py -> build/lib/repESP
copying repESP/graphs.py -> build/lib/repESP
copying repESP/rep_esp.py -> build/lib/repESP
...
Using /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages

•check you are upto date with "git fetch --all ; git pull"

  • make sure you can access all the scripts by adding to your PATH"export PATH=$PATH:your_scripts_path"
mine is "export PATH=$PATH:/Users/$USER/bin:/Users/tricia/bin/repESP/scripts:"
  • check that it is all working by "average.py -h" calling the help menu of average.
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