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Glycam Extensible Modeling System
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Installing GEMS (GLYCAM Extensible Modeling Script)

Obtaining the software
Compiling and Installing
Testing the Installation
Example Use


In order to install GEMS, you will need to have the following software available on your system:

  • openssl
  • git
  • python
  • python-dev (you need the Python header files for your Linux distro, which may not be part of your existing Python package)
  • swig
  • Kernel headers (the source code for the Linux kernel, which may not be installed on your system)
  • qmake
  • qt4-dev-tools
  • boost

NOTE - installing some prerequisites may require root access.

Installation instructions will vary according to the package management software your distro uses. If you use Ubuntu or any other Debian based system, you should be able to use a command like this:

sudo apt-get install openssl git python3 python3-dev swig build-essential qt4-qmake qt4-dev-tools libboost-all-dev 

For other Linux distros, please follow the instructions for the package management software included with your system.

Obtaining the software

Once you have installed the prerequisites, you can install the GEMS software.

NOTE - installing GEMS does not require root access.

Change to the directory where you will install GEMS, and clone the GEMS repo from Github:

git clone

This will create a gems directory. Change to the gems directory, and clone the GMML repo from Github:

cd gems/
git clone

Compiling and Installing

To compile the software, make sure you are still in the gems directory:


Set your PYTHON_HOME environment variable to the location of the Python.h file for your Python version. For Ubuntu, use something like one of the following:

export PYTHON_HOME=/usr/include/python3.4
setenv PYTHON_HOME /usr/include/python3.4

Make sure to use the correct path to your Python version, and the correct version of Python.

For other Linux distros, please follow the instructions to set environment variables specific to your system.

To control the number of processors used during the make process, set the GEMSMAKEPROCS environment variable.
The default value of 4 will be used if you do not set this variable. For exmaple, a command like one of the will set the number of processors to be used during make to 8:


After setting the PYTHON_HOME, run the makefile in order to compile gmml and create the gems interface.


Testing the Installation

Make sure you are still in the gems directory, and run the following command to test the installation:


The output will tell you whether the installation was successful or not and will look similar to this:

$ ./test_installation.bash

This test should take less than 10 seconds to run on most modern computers.

This test will compare these files:
        updated_pdb.txt -- this is the file the test should generate -- this is the file to which it should be identical

Beginning test.

Checking for diffeences between test output and the standard output.

The test passed.

NOTE - the test suite is a Bash shell script. Bash is generally installed by default on most Linux distros. If you try to run the test suite and get any errors, make sure that Bash is installed with the which bash command. This should return the $PATH variable for the bash executable, such as /bin/bash. If you get nothing back, you will need to either install Bash (which is far outside the scope of this README) or contact your system administrator for assistance.

Example Use

Make sure you are still in the gems directory, and run the following command, which is all on one line:

python3 -amino_libs "gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminoct12.lib" -prep "gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep" -pdb "gmml/example/pdb/Small_to_test.pdb" > testing.log 2&> testing.error

NOTE - make sure to use your version of Python.

There are also sample commands located at the top of the *.py files. Look in the comments for a line that says # SAMPLE COMMAND and use the examples found below there.

You can also use the available help for most GEMS functions.

$ python3 --help
Available options:
-amino_libs : amino acid library file(s) (e.g. gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib)
-glycam_libs: glycam library file(s)
-other_libs : other kinds of library files
-prep       : prep file(s) (e.g. gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep)
-pdb        : pdb file (e.g. gmml/example/pdb/1RVZ_New.pdb)
-cnf        : configuration file as an argument. sample file format:


The official documentation for both GEMS and GMML can be found on the main GLYCAM website:


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