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README
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README
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============================
Prerequisites:
============================
Installing some prerequisites will probably require root access.
You need these packages to use GEMS:
* openssl
* git
* python
* swig
* kernel headers
* qmake
* qt4-dev-tools
* boost
Installation instructions will vary according to system. If you use
ubuntu, you should be able to use a command like this:
sudo apt-get install openssl git python2.7 swig build-essential qt4-qmake qt4-dev-tools libboost-all-dev
If you use another operating system, please check the installation instructions for it.
============================
Obtaining the software:
============================
The following does not require root access.
Change to directory in which you want GEMS to exist
1. Get GEMS from git repo
git clone https://github.com/GLYCAM-Web/gems.git
2. Change directory to gems
cd gems
3. Get GMML from git repo
git clone https://github.com/GLYCAM-Web/gmml.git gmml
(you need the repo to be gmml rather than GMML as with the default clone)
============================
Compiling and Installing:
============================
1. You should still be in the gems directory.
2. Run make.sh file in order to compile gmml and create gems interface
./make.sh
============================
Testing the Installation:
============================
Testing the installation requires BASH. This is already installed on most
systems. If the command "which bash" returns no information, contact your
system administrator.
1. Run the following command:
./test_installation.bash
2. See the output.
============================
Example Use:
============================
Make sure you are still in the gems directory where you typed make and tested
the installation.
1. Try the command that was used for the test:
python2.7 pdbpreprocessing.py -amino_libs "gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-0
4-24/aminont12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminoct12.lib" -prep "gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLY
CAM_06j-1.prep" -pdb "gmml/example/pdb/Small_to_test.pdb" > testing.log 2> testing.error
2. Try similar sample commands at the tops of files named *.py. They will
be in the comments near the top of the file and will come just after
a line that says "#SAMPLE COMMAND :".