PURPOSE: Performs a gentle minimization on a protein molecule using CHARMm
This is a modified version of the standard Minimization protocol. It includes 3 stages of minimization:
1. Minimize just hydrogen atom while all heavy atoms are fixed
2. Minimize all hydrogens and sidechain atoms while all backbone atoms are fixed
3. Minimize all atoms

Note the protocol parameters such as 'Max Steps' are used to set the minimization at each of the three stages.

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 Gentle Minimization.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Embedded Collection. In order make use of all steps listed above, this protocol requires CHARMm or CHARMm Lite licenses.

KEYWORDS: minimization, heavy, protons, backbone

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.5 and Pipeline Pilot server version 7.5.2 (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.