1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/csp.zip
5. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to csp_tutorial, click Save
   • The project is now named csp_tutorial.prj

Figure 3-1. Using the 2D-Sketcher to draw acetaminophen.

We first need to draw a starting molecule. The molecule could be drawn in 2D or 3D using various MS Maestro tools, or can be imported from a file. In this case we will use the 2D Sketcher:

1. Go to Edit > 2D Sketcher
   • The 2D Sketcher panel opens
2. Draw the structure of acetaminophen

 

The 2D sketcher functions like many standard 2D molecular drawing tools. For a complete overview of using the sketcher panel, see the 2D Sketcher Panel documentation or watch the Building Small Molecules video in the Getting Going with Materials Science Maestro Video Series.

3. Click on Save as New and for Input Entry Title write acetaminophen. Click OK

Figure 3-2. Viewing acetaminophen in the workspace.

4. Close the 2D Sketcher panel
   • The acetaminophen molecule is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

If preferred, change the representation to ball-and-stick by clicking on the Style menu and choosing Apply ball-and-stick representation

 

Figure 3-3. Opening the Crystal Structure Prediction panel.

5. With the acetaminophen entry selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue, go to Tasks > Materials > Polymorph Prediction > Crystal Structure Prediction
   • The Crystal Structure Prediction panel opens

Figure 3-4. Running the Crystal Structure Prediction panel to generate conformers.

6. Change the Task to Generate conformers only
   • Running a conformers job first is best practices to ensure the conformers are what you’d expect before moving to the much longer packing and ranking calculation
7. Click Load to load the molecule
   • Acetaminophen will now be loaded into the panel
8. Change the Job name to csp_conformers
9. Adjust the job settings () as needed
   • This job requires a CPU host and should complete in a couple of minutes on 8 CPUs
   • Job Server is required for submission of Crystal Structure Prediction calculations
10. Click Run or import the file from the provided tutorial files
11. Close the Crystal Structure Prediction panel

Figure 3-5. Running the Crystal Structure Prediction panel on the acetaminophen conformers.

12. When the job is finished, a new entry titled output_confgen is automatically  included in the entry list
13. With the output_confgen group selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries, use the Workflow Action Menu (WAM) button () or go to Tasks > Materials > Polymorph Prediction > Crystal Structure Prediction
    • The Crystal Structure Prediction panel opens
    • The panel will automatically populate by default with all 11 acetaminophen conformers
14. Change the Job name to csp_acetaminophen
15. Adjust the job settings () as needed
    • This job requires a CPU and GPU host. The job can be completed in five days using 32 CPUs and 1 GPU. However, this calculation runs thousands of subjobs. Specifying 10,000 CPUs is ideal but will use many resources at once. A balance needs to be achieved between wall time and the use of resources.
    • Job Server is required for submission of Crystal Structure Prediction calculations.
16. If you would like to run the job, click Run, otherwise, we will proceed with pre-generated results in the next section
17. Close the Crystal Structure Prediction panel  

The calculation will pack the conformers into unit cells by using various space groups and then relaxing the structures and filtering out the highest-energy ones. The relaxation part does a series of relaxations, each of which is followed by a filter. The first uses molecular mechanics (MM) (cheapest), then machine learning force field (MLFF) (medium), then density functional theory (DFT) (most expensive). So there are less crystals that need to do DFT run on them than MM. When the include DFT ranking box is checked the DFT ranking results are returned.

In this example, the Generate missing parameters option is automatically removed upon loading the molecule because no torsions are missing. However, if the molecule had torsions missing, that box would have the option to be checked. Then there would be an option to use a customized version of the forcefield.

Figure 4-1. Opening the Crystal Structure Prediction Viewer panel.

1. From the main menu, choose File > Import Structures
2. Navigate to where you downloaded the tutorial files and choose Section_03 > csp_acetaminophen > output_qrnn_relaxation.maegz file
3. Click Open
   • A new group with 2415 structures is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. The entire group is automatically selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and the first entry is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
   • Maintain the entire entry group selection
4. Use the WAM (workflow action menu) button () to open the CSP Viewer
   • Alternatively, go to Tasks > Materials > Polymorph Prediction > Crystal Structure Prediction Analysis
   • The Crystal Structure Prediction Viewer panel opens

Figure 4-2. Clicking and viewing the data points.

5. Click the data points to view information about the structure

Each dot corresponds to one crystal structure and appears as a new entry in the entry list and the packing arrangement is shown in the workspace

Figure 4-3. Viewing the results in data table form.

6. Go to the Data Table tab

Scroll across the data table to view information about each crystal structure. There are two known experimental crystal structures and both are found here. The first has density 1.349 and spacegroup P121/n1. The second has density 1.382 and spacegroup Pbca. Feel free to explore the results and close the panel once finished.