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
XP Atom Energies

Adds Glide XP terms from .xpdes file to a Maestro file as atom-level properties. These properties can be used to color and visualize atoms by the values.
Create or Convert Pose Viewer Files

Converts pose viewer files into a series of complexes, and convert complexes into ligand-only, receptor-only, or pose viewer files.
Compute Entropy Associated with Each Energy Well

Computes a modified docking score based on work by A.M. Ruvinsky using the number of poses within each energy well. Poses are first clustered and then the entropy is computed for each cluster. Input poses should come from Glide saving 100 poses per ligand. The criteria for duplicate pose elimination should be reduced to zero (in the Clustering section under Advanced options in the Output tab of the Glide Docking panel) in order to ensure a full sampling of each energy well.
Score and Filter Docked Fragment Poses from Glide

Takes a Glide poseviewer file as input and outputs the top poses based on a ligand efficiency metric and spatial diversity.
Generate Rotamer Conformations for a Given Residue

Generates rotamer conformations for the given residue in an input structure file with each conformation written to the output file (Maestro format only).
Create Residue Scanning Mutation File

Creates an input file that can be passed to the residue scanning backend via the -muts_file option.
Compute NMR Chemical Shifts

Computes Boltzmann averaged chemical shifts from NMR shielding parameters and an ensemble of conformers.
Compute Consensus Scores

Combines scores from multiple virtual screening calculations using various data fusion methods. Screening methods include docking (Glide), shape (Shape Screening), and fingerprints (Canvas). Data fusion methods include Z-score, parallel selection, rank vote, sum rank, sum score, and Pareto.
Generate Crystal Mates

Generates crystal mates using crystallographic information from the PDB file.
Delete Atoms from a Structure

Deletes atoms from a structure file based on a Maestro ASL expression.
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