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
Grid Generation from Poseviewer File

Generates a Glide grid from a poseviewer file. The ligand in the poseviewer file is used to determine the center of the Glide grid box.
Create Glide Simplified Input File

Takes command line options and creates a Glide simplified input file (SIF).
Calculate Entropy

Calculates the entropy and Boltzmann-weighted energy (in kJ/mol) for a multi-entry file. The temperature (in K) can be adjusted and the relative energy property can be specified.
Compare Ligand Ranks

Compare ranks of compounds in structure files that are ordered in ascending rank (best first).
Split Structure by Substructure

Splits structures by chain, molecule, residue, ligand or PDB.
Compute Ligand Volume

Computes the volume for each ligand or active site in a file.
Find Receptor-ligand Interactions

Detect interactions between a receptor and a set of ligands in a poseviewer file. The script lists each H-bond and contact (good, bad, or ugly) along with a summary reporting the number of ligands forming each kind of interaction with each receptor residue. The script also detects hydrophobic, salt-bridge, pi-cation, and pi-pi interactions.
Block-sort Glide Results

A command-line script for block-sorting Glide results, in which the results for each ligand are grouped and sorted by Emodel (HTVS/SP) or the XP pose rank, and then the ligand blocks are sorted according to the GlideScore of the top member.
Compute SASA of Ligands in a Complex

Estimates the solvent accessible surface area (SASA) of a ligand or pose in the context of a receptor.
Binding SASA

Calculates SASA of ligand and receptor before and after receptor-ligand binding.
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