Inspired by a couple of recent support cases and a protocol posted in the Pipeline Pilot community:

https://community.accelrys.com/message/2928,

Please find a simple protocol that reads in a series of Input Ligands from your Molecule Window (or from a SD file) and splits the data into multiple SD files. 

INSTALLATION: 

In your Discovery Studio 3.1 Client, navigate to the Protocols Explorer tab, select your username's folder, right click and choose the Import command.  Select the attached XML file.

You can also open this protocol in the Pipeline Pilot 8.5 client.

USAGE:

The user has 2 options:

1)

Split Into Files With Equal Number of Ligands = TRUE

Number of SD Files = user-defined

This option will allow the input dataset to be equally split across a set number of SD files.  For example, if you start with 1,000,000 molecules and set the number of SD files to 100, each SD file will contain 10,000 molecules.

2)

Split Into Files With Equal Number of Ligands = FALSE

Number of Ligands in Each Output SD File = user-defined

This option will prompt the user to specify the number of ligands required in each output SD file.  The protocol will create the required number of SD files automatically.

DISCLAIMER:

This custom protocol is compatible with Discovery Studio 3.1. It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.

REQUIREMENTS:

Discovery Studio 3.1 Client and Server or Pipeline Pilot 8.5 Client and Server

EXPECTED RESULTS:

After running the job from Discovery Studio 3.1, the Output directory will include the standard Report.html along with a series of SD files named outputXXX.sd