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1. Double click the Maestro or Materials Science icon to start Maestro or MS Maestro
   • No icon? See Starting Maestro
   • This tutorial uses MS Maestro, but this workflow can be performed in Maestro or MS Maestro. Use whichever interface you are comfortable with or typically use for your projects.

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/complex_protein_solutions.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 protein_solutions_tutorial, click Save
   • The project is now named protein_solutions_tutorial.prj

Figure 2-3. Five entries in the entry list to be used as the components in the subsequent sections.

We will proceed to import the components that we will use in the subsequent sections: Tween 20, sucrose, water, a chlorine anion, and a sodium cation. If you would prefer to draw or build these components yourself using the 2D Sketcher and the Polymer Builder, feel free to do so following similar steps outlined in the Introduction to Materials Science Maestro tutorial. Otherwise:

8. Go to File > Import Structures
9. Navigate to where you have downloaded the provided files (presumably in your working directorythe location where files are saved), and choose the excipients_water.maegz file
10. Click Open
    • A new entry group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion entitled components (5) containing the five entries

Figure 3-1. The Protein Preparation Workflow panel.

Let’s start by importing and preparing the protein of interest.

1. Go to Tasks > Browse All > Protein Preparation and Refinement > Protein Preparation Workflow
   • The Protein Preparation Workflow panel opens
2. Click Get PBD

Figure 3-2. Importing the 2JOF PDB file.

3. For PDB IDs, type 2JOF
   • Trp-cage (2JOF) is a small protein
4. Click Download

Figure 3-3. The 2JOF PDB structure.

28 configurations of the PDB structure 2JOF have been loaded into the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The top entry will be used in this panel setup.

Figure 3-4. Running the Protein Preparation Workflow panel.

5. Change the Job name to proteinprep_2JOF
6. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed almost instantly.
7. Back in the Protein Preparation Workflow, click Run

Figure 3-5. Fully prepared 2JOF.

A new entry group and structure have appeared in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled 2JOF-prepared, and 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 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. This structure is the fully prepared protein structure.

Feel free to visualize and stylize the structure in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. In the new entry only polar hydrogens are shown. Going to Style > Show all Hydrogens to view all the hydrogen atoms.

Figure 4-1. The entries selected and the Disordered System Builder panel open.

1. Select(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 the five excipients_water entries: tween 20, sucrose, water, Cl_ion and Na_ion from the entry list
2. Includethe entry is represented in the Workspace, the circle in the In column is blue the 2JOF-prepared entry
3. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • The five selected components are by default loaded into the panel
   • If you see different components or additional components, revisit Step 1

Figure 4-2. Setting the components.

4. For Initial state, choose Amorphous
5. Change Number of molecules to 4569
6. In the Components table, change the Number of molecules for tween 20 to 4, sucrose to 40, water to 4500, Cl_ion to 12, and Na_ion to 13
   • An additional Na ion is required to neutralize the overall system charge due to the protein structure's -1 charge.
   • The wt% appears in the panel and the table updates interactively
7. Check the Substrate box
8. Import the included entry 2JOF - prepared
9. Ensure that Substrate type is Immersed
10. For Periodic Boundary Conditions (PBC), choose Create new cubic PBC

 

Note: Building complex protein systems, especially larger ones, presents significant challenges. For instance, if protein concentrations are above 20 wt%, the calculations can take significantly longer. Simply adding more water molecules to the system would likely increase the building time linearly, assuming a consistent target density.

 

However, the introduction of excipients complicates the system. If excipients are large, flexible, or present at high concentrations, the process can quickly become impractical. As protein levels, or the concentration and size of excipients, increase, calculations become more difficult.

 

If issues arise, consider separating the excipients from the solvent addition or building the system at lower densities. In such cases, the Solvation Builder can efficiently handle solvent addition for large systems.

Figure 4-3. Running the job.

11. Go to the Disorder tab
12. Uncheck the Color molecules by component box
13. Set the Initial density to 0.200
14. Change the Job name to disordered_system_trp_cage_excipients
15. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 5 minutes on a CPU host.
16. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_04 > disordered_system_trp_cage_excipients > disordered_system_trp_csge_excipients-out.cms file from the provided tutorial files via File > Import Structures
17. Close the Disordered System Builder  

Figure 4-4. Output of the Disordered System Builder in the workspace.

When the job is complete, a new entry group will be incorporated titled MD: disordered_system_trp_cage_excipients_system (1) containing one entry titled disordered_system_trp_cage_excipients_all_components_amorphous

18. Includethe entry is represented in the Workspace, the circle in the In column is blue the new entry
    • The box is visible in the workspace
    • The components are colored by default, but feel free to stylize as you wish
19. Use the WAM button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Figure 4-5. Setting up the MD Multistage Workflow.

20. Check Relaxation protocol and choose Constant pressure
21. Change the next stage (Stage 6) to Molecular Dynamics
22. Set the Simulation time (ns) to 80
23. Set the Trajectory Recording interval (ps) to 160
24. Change the Job name to multistage_simulation_trp_cage_excipients
25. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 3 hours on a GPU host
26. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated Section_04 > multistage_simulation_trp_cage_excipients > multistage_simulation_trp_cage_excipients-out.cms file from the provided tutorial files via File > Import Structures
27. Close the MD Multistage Workflow panel

Figure 4-6. Output of the MD simulation.

28. When the job is finished or after importing, select(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 includethe entry is represented in the Workspace, the circle in the In column is blue the new disordered_system_trp_cage_excipients_all_components_amorphous entry from the entry list
    • In the Figure the hydrogen atoms are hidden to better visualize the protein and excipients

Feel free to visualize the Trajectory if you are interested by clicking the . For additional analysis, refer to the Diffusion or Cluster Analysis tutorials. Alternatively, proceed to the Creating a Coarse-Grained Model for Protein Formulations tutorial to run a CG simulation on the system.