To improve the efficiency of the ligand building procedure, the quantum chemical (QM) calculations can be out-sourced to dedicated programs. This is a achieved by the user putting a shell script file in their $HOME that will run the QM program. An example of a GAMESS script is given in $PHENIX/elbow/GAMESS.csh.
Copy this file to your home directory (or edit it in place but the $HOME copy takes precedence).
Edit the file to reflect the local environment making sure to retain the two %s format statements. The first is given a project name and the second is the current directory which is useful in batch mode.
To run elbow:
elbow.builder --gamess --smiles "FOO"
or:
elbow.builder --gamess --file chemical_input_format_file.ext
Upon a successful conclusion, there will be an elbow.LIG.pdb and elbow.LIG.cif file in the current directory.
Currently, GAMESS, Gaussian and MOPAC are explicity supported by there are mechanism for using other packages.
For a complete list of builder options (expert options here)