PURPOSE: Demonstrates a customized protocol built with existing simulation components such as the CHARMm Minimization, CHARMm Heating and CHARMm Production components. A typed molecule is first minimized by two different minimization algorithms, then subjected to heating and cooling dynamics, and optionally production simulations and finally another minimization. The output from the final minimization is used as input for the next cycle of minimization and dynamics. The output from each cycle consists of trajectories and minimized structures stored as dsv files.
The final minimized structure from each cycle has the extension "#_finalMin.dsv". If Perform Production is set to true, the output will have a "#_prod.dsv" file containing the trajectory of the Production dynamics stage for that cycle. If Perform Production is set to false, then the output will have a "#_heat.dsv" file containing the trajectory of the last cooling dynamics stage in that cycle. All final minimized conformations for each cycle are stored in one dsv file called 'min_conformations.dsv'.

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 Simulated Annealing Cycles.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Embedded Collection. DS CHARMm

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.5 and Pipeline Pilot server version 7.5.4 (SES). 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.