Jobcontrol 1-2
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
MD simulation 1
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
Grid generation 1-2
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Group looper
Illustrate how to iterate over structures in the input table with two different looper implementations. Extract the second lowest energy conformer of each […]
Run PyMOL 1
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
Binding Pose Metadynamics
Various binding configurations of a single ligand in a single binding site are ranked.
Grid generation 1
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
ESP 1-2
Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Requires: LigPrep, Jaguar]