This option allows the expert user to use a external program to optimise the ligandgeometry. Alternatively, the user can write a couple of Python modules and contribute them to the e-LBOW code. For information on this more integrated method contact the author.
The general steps involved in using an external optimisation program via the --user-opt are as follows:
elbow.builder writes a XYZ file
elbow.builder calls a program provided by the user to convert the XYZ file to a input file to the external program
elbow.builder calls a program or script provided by the user to run the external program
elbow.builder calls a program provided by the user to convert the output from the external program to a XYZ file
elbow.builder reads the XYZ file and continues
The conversion programs to and from XYZ can be written in Python and examples are provided in the e-LBOW code directory tree. Running:
elbow.builder --key ehn --user-opt
will lead the user through the process and required inputs.