If you have a dynamics trajectory MSV file from a CHARMm MD simulation and you want to run minimization of the trajectory frames, you can use this simple Pipeline Pilot protocol to read in the MSV file and minimize each frame, or every Nth frame, (user can specify the parameter N,) and all the minimized structures are saved as individual molecules in one MOL2 file in a user-specified directory.
This protocol should work in both DS 1.7 and DS 2.0. The Source parameter in the protocol is for you to browse to read in your trajectory MSV file, and the Destination parameter is for you to enter a name of the output MOL2 file. User can also specify the minimization parameters: Minimization Algorithm, Max Steps, Implicit Solvent Model etc.
Note that in DS 2.0 Client now you can right-click on your
