PURPOSE: Given a Directory Path, this protocol will:
1. Read in all PDB files from the specified directory
2. Remove all objects that are not Nucleic Acid chains from the molecular system (i.e. water, ions, ligands, etc.)
3. Add hydrogens to the remaining chains
4. Add intermolecular hydrogen bond monitors
5. Output a separate .csv file for each input pdb file reporting the hydrogen bond properties such as the Intermolecular HBond Name, Distance, Angle HDA and Angle HAY
6. Output a summary .csv file for each input pdb file reporting the average Distance and Angle values for each Base Pair.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Intermolecular Hydrogen Bonds for Nucleic Acid Systems.xml file and enter it as the File Name.

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.1 and Pipeline Pilot 6.1.6. 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.