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To download the Schrödinger software, please visit the Download Center (login required):


As of September 8, 2017, the current release version is 2017-3 (just released yesterday!).

Just in case, I have a copy downloaded already for Windows and MacOS, which will be provided either by USB key or CD.

It may take a while to download given its large size (about 4GB).

  Now take a break ... while downloading

Installation on your laptop

Before we start, make sure you are within the Case campus network, either by connecting through


If you are using the CaseGuest wireless, you may need to activate



Start by

  1. Double-clicking setup.exe 

Wait for several seconds ... follow the instruction by clicking some 'yes' or 'next' buttons.

  2. "Installing software" ... and wait (depending on how old your laptop is) 

... after several minutes (hopefully), then clicking more 'next' using the default (unless you know what you are doing).

When you see

    "Installation completed successfully!" ... 

STOP and click


Since we have been issued a license (installed on a server) , choose

   Add Licenses [I can identify my license server]

Enter Host Name:


and Port



   Replace XXXX with the code provided on-site


   click "Save Server". 

Then check the "Current Status" above. If you see

  "Valid licenses found" 

Congratulations! You are ready to play.

Mac -- License Installation Instructions

After installation, use

  Finder, navigate to Applications → SchrodingerSuites2017-3. 


   Open the Configuration application by double-clicking on it.

Since we have been issued a license (installed on a server) , choose

   Add Licenses [I can identify my license server]

Enter Host Name:


and Port



   Replace XXXX with the code provided on-site


   click "Save Server". 

Then check the "Current Status" above. If you see

  "Valid licenses found" 

you are good to move on.

Getting familiar

Introduction to Structure Preparation and Visualization

This gives an introduction to the Maestro interface and basic visualization tasks. You will learn how to prepare ligand and protein structures, an essential first step for modeling projects.

    using a 3-button mouse with a scroll wheel

Creating Projects and Importing Structures

  Navigate to File > Get PDB

Visualizing Protein-Ligand Complexes

We will explore ways to visualize structures in the Workspace.

Protein Preparation Wizard

The Protein Preparation Wizard will automatically take care of many protein preparation tasks.

To open the Protein Preparation Wizard panel,

  choose Tasks → Protein Preparation and Refinement → Protein Preparation Wizard in the Task Tool, 


  click the Protein Preparation Wizard button on the Favorites toolbar (if present).

Import and Process tab

To preprocess the structure, select the desired options, then click


The options are as follows:

  • Align to—Align the protein structure to that of another protein. You can choose the other protein by selecting an entry in the Project table (Selected entry) or by specifying a PDB ID for a structure from the PDB. The alignment is done with the Protein Structure Alignment tool that is on the Tools menu—see <a href="../prime_help/protein_structure_alignment.html" class="MCXref xref">Protein Structure Alignment Panel</a>.

  • Assign bond orders—This option selects the assignment of bond orders, and performs the same task as Assign Bond Orders on the Tools menu.

  • Add hydrogens—This option adds hydrogens to all atoms in the structure that lack them. The hydrogens are added by the utility applyhtreat.

  • Remove original hydrogens—This option removes the original hydrogens before hydrogens are added, and is only available if Add hydrogens is selected. It ensures that any problems with H atoms are fixed, including nonstandard PDB atom names, which is important for the H-bond optimization tool.

  • Create zero-order bonds to metals—This option breaks bonds to metals, replacing them with zero-order bonds, and adjusts the formal charge on the metal and the neighboring atoms. Sulfurs that interact with metals have their hydrogens removed, if necessary, and are assigned a negative charge. The force fields usually treat metals formally as an ion, without bonds to their ligands.

Review and Modify tab

The goal is to fix Protein Structural Problems if any.

E.g. To add missing side-chain atoms:

 View Problems → Add missing side chains → OK

Refine tab

The goal is to minimizing the Protein Structure.

When you have made your selection of options, click


Receptor Grid Generation

The Receptor Grid Generation panel is used to specify a receptor structure and set up the grid generation job. This job creates the grid files, which represent the active site of the receptor for Glide ligand docking jobs.

To open this panel, choose in the Task tool

  Receptor-Based Virtual Screening → Receptor Grid Generation.

The Receptor Grid Generation panel contains five tabs, which are described in full in separate topics:

  • Receptor tab— Use this tab to define the receptor (by identifying the Workspace ligand, if one is present) and optionally to scale the van der Waals radii of receptor atoms.
  • Site tab— Use this tab to determine the position and size of the volume for which grids will be generated, representing the active site of the receptor.
  • Constraints tab— Use this tab to designate certain receptor atoms (positional/NOE, H-bond/metal constraints) for ligand-receptor interactions that you can then choose to require during docking jobs.
  • Rotatable Groups — Use this tab to specify groups that should be treated as rotatable in the grid generation. These groups are currently restricted to hydroxyls in Ser, Thr, and Tyr, and thiols in Cys.
  • Excluded Volumes— Use this tab to set up regions of space in which the ligand is penalized during docking.

Two scenarios:

Ligand bound

Known pocket but without no ligand bound

Ligand preparation