Optional Advanced Features

RMG has a number of additional features available which enable advanced functionality but require additional installation steps. The following sections discuss the additional features available in RMG and the dependencies and installation procedures for each.

InChI Generation

RMG can be configured to work with the IUPAC International Chemical Identifier (InChI) format for representing molecules. When InChI support is enabled, RMG can generate InChI strings for molecules and convert from InChI strings and/or .mol files to the adjacency list format. To enable InChI support you must download and install the following:

The IUPAC International Chemical Identifier InChI version 1

Version 1.02beta is required. This is available from http://www.iupac.org/inchi/download/index.html.

For Windows, in the 1.02beta download package, navigate to the cInChI/vc6_project/Release directory and copy the file:cInChI-1.exe executable to the $RMG/bin folder.

For Linux, after downloading and unpacking the InChI source code, change to the InChI-1-API/cInChI/gcc_makefile directory and execute the makefile. Copy the resulting executable cInChI-1.exe to the $RMG/bin folder.

$ cd InChI-1-API/cInChI/gcc_makefile
$ make
$ cp cInChI-1 $RMG/bin

You are now ready to generate InChIs in RMG.

Sensitivity Analysis

RMG can optionally perform sensitivity analysis on the reaction models it generates. Currently RMG uses DASPK 3.1 to perform sensitivity analysis. Analytical Jacobian and partial derivatives with respect to rates of reactions and Gibbs free energy of molecules are generated using the automated differentiator of DAEPACK.

1. Make sure the DAEPACK library file is in a location where the Fortran linker can find it. On Linux, you can either make a symbolic link of the library file in a directory in your library file search path, e.g. /usr/lib, or add the path containing the library to the LD_LIBRARY_PATH environment variable.

2. Compile DASPK using the command

   $ cd $RMG
   $ make daspk

You are now ready to run RMG with sensitivity analysis support.

3D-geometry-based Thermodynamic Property Calculation

RMG can optionally use quantum chemistry calculations to estimate the thermodynamic properties of the species it generates. This feature requires several additional dependencies, including either the Gaussian 03 or MOPAC 2009 quantum chemistry package. These dependencies are:

Python

Version 2.5, 2.6, or 2.7 of Python is recommended. On Windows you will probably need to manually add the directory containing the python binary to the PATH environment variable.

NumPy

Version 1.3.0 or later of NumPy is required.

RDKit

Version Q2 2009 or later of RDKit is required. The typical installation process for RDKit should set the RDBASE environment variable and no further action on the part of the user should be required. On Windows you will also need to set environment variables as described here.

OpenBabel

Version 2.2.0 or later of OpenBabel is required. On Windows the OpenBabel installer should update the PATH environment variable automatically.

InChI

Version 1.02beta is required. Installation instructions are as given here. Don’t forget to place the InChI executable in the $RMG/bin directory.

SYMMETRY

Version 1.15 or later of SYMMETRY is required. The SYMMETRY.EXE executable should be placed in the $RMG/bin directory. A pre-compiled Windows binary executable is available via the symmdos.zip file found in the aforementioned web folder.

MOPAC 2009

Available at http://openmopac.net/downloads.html. MOPAC may be obtained freely for academic, not-for-profit use. You only need to install one of MOPAC 2009 or Gaussian 03, though having both can be advantageous for handling troublesome cases.

On Windows, use the download called MOPAC2009 for DOS under any Windows; the installer should set the MOPAC_LICENSE environment variable automatically.

On Linux, you will need to set the MOPAC_LICENSE variable manually

(e.g. export MOPAC_LICENSE=/opt/mopac/ in .bashrc or before each time RMG is run with MOPAC calculations).

Gaussian 03

The Gaussian web site is http://www.gaussian.com/. On Windows you will likely need to manually update the PATH environment variable to include the Gaussian installation directory.

A modified version of cclib based on the cclib 1.0 release is also included with RMG; you do not need to download this separately.