Name: Clean and protonates files from the PDB ( protein only or complexes ) using calculated pKa for the protein
Author: Anne GOUPIL
Version: 1.0
Created: 3/2008

Purpose: This protocol can be used to "clean" and protonate a complex that comes from the PDB. Water molecules are removed for the pKa calculation. The CLeanProtein function from Discovery Studi is used with the following options:
CleanProtein( { HydrogenRepresentation =>'allHydrogenRepresentation', pH =>7.0, AdjustHydrogens =>True, DeleteDisorder =>True, StandardizeNames => True, CompleteResidues => True } );

Requirements: Pipeline Pilot 6.1, Discovery Studio 2.0 or 2.1
O/S: Windows and Linux
Limitations: none known

Installation:

1. Import the protocol into your user tab in the Discovery Studio or Pipeline Pilot client by dragging and dropping it in the Explorer window
2. You can either run it from Discovery Studio or Pipeline Pilot client