If your ligand contains amino acids and you dock it using CDOCKER you will find that all the properties associated with the amino acids such as type, hydrophobicity etc. are lost in the output files. The reason is the ligand poses are saved in sd file format and that format doesn't have fields for residue-based properties. Fortunately, the attached script allows you to restore that information to the output poses using the input ligand file. 
First, from the DS Client open the output file from the CDOCKER job containing the protein and ligand poses. Next, from the Files Explorer, right-click on the RePeptideDockedLigand.pl file and select Open With | Script Window. Edit the line in the script which specifies the location of the input ligand file. That line is found under the comment line "ADJUSTABLE PARAMETERS". Finally, launch the script using the Run command from the Scripting toolbar or the context menu.

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