This is the latest version of the Binding Free Energy - Single Trajectory protocol for use with DS 2022.
The input for this protocol is a trajectory from a molecular dynamics simulation which was performed on
some complex (i.e. a protein-ligand complex or a protein-protein complex). This protocol then performs three single energy calculations:
(a) on the complex
(b) on one body/part of the complex
(c) on the remaining part of the complex
The following energy is calculated for each frame:
Gbinding = G(a) - G(b) - G(c)
Then the average of Gbinding is calculated over all frames and reported as the DeltaG_Average.
The user specifies whether to use an Implicit Solvent Model and other forcefield simulation parameters. The system you specify as the 'Input Typed Molecule' should NOT contain solvent.
One important improvement over previous version is this latest version supports nucleic acid chains. However, be sure to specify those chains as the Ligand Chains.
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 Binding Free Energy - Single Trajectory.ppxml file and enter it as the File Name.
DISCLAIMER: This custom protocol is compatible with Discovery Studio 2022 and Pipeline Pilot server version 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.
