All of the scripts listed on this page come pre-bundled with the latest Schrödinger Software release. To use any of these scripts simply use the following instructions:

Linux - In a Terminal Window type: $SCHRODINGER/run <> -h
Mac - In a Terminal Window type: $SCHRODINGER/run <> -h (Note: $SCHRODINGER Environment Variable must be set)
Windows - In a Schrödinger PowerShell Window or in the Schrödinger Command Prompt type: run <> -h

For more information, please visit Knowledge Base Article 37 or view our Documentation on Running Jobs From the Command Line.
Script Requires
Restrained MacroModel Minimization using B Factor Constraints

Sets up restrained MacroModel minimizations of systems with constraints set from the X-ray derived B factors.
Final All-Atom Polish Refinement

Produces an all-atom model that is consistent with the diffraction data and force field parameters, starting with an initial refined crystal structure. It applies reciprocal-space optimization of coordinates and thermal factors, simulated-annealing refinement, and hydrogen-bond optimization in an automated manner. The script can generate ionization/tautomer states for the ligands and protein. The various optimized complexes are then assessed as to the complementarity between the ligand and the protein using the Schrödinger docking program Glide. The model selected as best is treated to three final cycles of automated refinement.
QSite Binding Energies

Performs a QM/MM-PBSA calculation to compute binding energies for one or more ligands from a poseviewer file.
Shape Screen Cluster

This script is intended for use as a workflow for clustering based on shape_screen analysis. In addition to the shape_screen output files, clusters are written out as maestro files and a cluster_data.csv file containing the clusters as lists of structure titles.
Shape Screening
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