LigandParameterizationParallel workflow

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This workflow parameterizes small molecules in parallel. It takes a list of pdb files stored in a local directoryand creates corresponding sub-directories using the pdb file names. Parameterization of each small molecule willbe done on corresponding sub-directories using Amber tools (antechamber, tleap) and Gaussian09. The final output is anew pdb file named LIGAND_NAME-new.pdb which can be used for any further experiments and for validations.

Required Software

Kepler 2.4 or above
AmberTools 12 or above




There are two ways to run this workflow. One is through the graphic interface. After the workflow is opened,users can double-click the parameters to change their values and press the play button to start. Another way isto run Kepler via a command line. It is highly recommended that users check the values in StringConstant inside Parameterization Actor before running the workflow to ensure that the commands to executetleap are suitable for unique systems.


c charge of the small molecules. All the small molecules must have the same charges. Default is 0 whichmeans all the small molecules are neutral.

d directory with the small molecule pdb files.

p pattern of the pdb files. Default is .*pdb$$ which means all the pdb files in the directory.

p2 pattern of the pdb file to be replaced by empty string in order to obtain only the ligand name. Defaultis .pdb which means that LIGAND_NAME.pdb will turn into LIGAND_NAME

n the number of pdbs to parameterize in a single run. For example, if user has five small moleculesin a single directory that need to parameterize, n will be set to five.