TITLE:

Heat a Small Molecule, Minimize Each Conformation, and Cluster by RMSD

PURPOSE:

Use this custom protocol to run a CHARMm heating simulation followed by a CHARMm minimization of each conformation then cluster the conformations by RMSD on a small molecule.

CREDITS AND DESIGN:

The protocol was built using several default protocols available in Discovery Studio 2.0 (DS20): "Dynamics (Heating and Cooling)" and "Analyze Ligand Poses"

In addition, the forum posting by Tina Yeh entitled "Minimize a set of conformations from a MD trajectory"

https://community.accelrys.com/message/1202

was used to help design the minimization steps in this protocol.

INSTALLATION INSTRUCTIONS:

Install using your Pipeline Pilot Professional Client to your user tab.

Install using your Discovery Studio 2.0 Client. In the Protocol Explorer, right click on the username's folder, and select Import. Browse for the XML file.

USAGE:

This protocol is designed to run only from DS20 Client.

REQUIREMENTS:

Input 3D window with a single small molecule. The molecule will need to be typed with a CHARMm forcefield.

EXPECTED RESULTS:

The key output from this protocol will be a SD file of conformations derived from the simulation and minimization procedure. In the Output/RMSD subdirectory, you will find a perl script that will create a hierarchical cluster dendrogram based on the RMSD values across the conformations. This perl script needs to be run from the DS20 client

If you chose to keep the intermediate files for the DS20 preferences, additional files created during the steps of the simulation will be available.

ATTACHMENT CONTENTS:

1. 00README.txt -- the text shown here
2. The protoocol entitled "Heating_MinimizeConfs_ClusterConfsByRMSD.xml"
3. A sample output run directory on the "1qbu_ligand.sd" available in the Samples folder of your DS20 installation. All input, intermediate and output files are captured in the simple example.
4. Two screenshots views in DS20 where your ligand and dendrogram are side by side for easy viewing.

DISCLAIMER:

This custom protocol is compatible with Discovery Studio 2.0. 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.