PURPOSE: Performs a "gentle" minimization on a protein molecule using CHARMm. This could be used to further refine a homology model. The idea is if there are 'hotspots' in the structure, this approach can reduce the likelihood that those could cause large distortions throughout the molecule during minimization.
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 atoms while either CAlpha or all backbone atoms are fixed (see parameter "Stage 2 Constraint")
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 script is compatible with Discovery Studio 2022.  The code or software provided by Dassault Systemes Biovia Corp. ("BIOVIA") in conjunction with this request is provided under the same license terms and restrictions as the underlying BIOVIA software it is intended to be used with, including license duration and location based restrictions, with the following exceptions.  This software is provided on an AS-IS and AS-AVAILABLE basis with no guarantee or warranty, and is not subject to maintenance, updates, or support.  When your license to use the underlying BIOVIA software terminates, your license to use this software will also terminate.  BIOVIA makes no warranty that this software will be usable for any purpose.