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static M M
_Index snap(MM_Index corect, MM_Index ligct, int imatch0, int *moleatoms, i
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Conformational Analysis for Small Molecules Using MacroModel and ConfGen
Created with: Release 2018-2
Prerequisites: Release 2017-4 or higher Introduction to Structure Preparation and Visualization Mogul Configuration Setup
Required Files: TorsionalScanning.prjzip, ConformationsPeptide.prjzip, KFGLE.txt, Ddrive
Categories: Discovery Informatics, Structure Prediction and Analysis, Structure-Based Drug Design, Ligand-Based Drug Design
Keywords: torsional scan, minimization, clustering, energy barrier, PLDB
In this tutorial we will investigate tools that are useful for exploring conformational space, from small molecules to protein-ligand complexes.
Words found in the Glossary of Terms are shown like this: Workspace File names are shown with the extension like this: benzene.maegz Items that you click or type are shown like this: File > Import Structures
This tutorial is written using a 3-button mouse with a scroll wheel and consists of the following sections:
1. MacroModel Prerequisites - p. 1
2. Creating Projects and Importing Structures - p. 1
3. Scanning Torsions and Understanding Barriers - p. 3
4. Scanning Torsions for a Series of Molecules - p. 10
5. Generating Small Molecule Conformers - p. 18
6. Optimizing Conformations - p. 27
7. Clustering Methods - p. 29
8. Conclusion and References - p. 32
9. Glossary of Terms - p. 32
1. MacroModel Prerequisites Structure files obtained from the PDB, vendors, and other sources often lack necessary information for performing modeling-related tasks. Typically, these files are missing hydrogens, partial charges, side chains, or whole loop regions. In order to make these structures suitable for modeling tasks, we use the Protein Preparation Wizard to resolve issues. Similarly, ligand files can be sourced from numerous places, such as vendors or databases, often in the form of 1D or 2D structures with unstandardized chemistry. LigPrep can convert ligand files to 3D structures, with the chemistry properly standardized and extrapolated, ready for use in virtual screening. In this tutorial, the proteins and ligands have already been prepared in order to save time. However, these preparation steps are a necessary part of conformational analysis and must be done before using MacroModel. Please see the Introduction to Structure Preparation and Visualization tutorial for instructions on using the Protein Preparation Wizard and LigPrep.
2. Creating Projects and Importing Structures At the start of the session, change the file path to your chosen Working Directory in Maestro to make file navigation easier. Each session in Maestro begins with a default Scratch Project , which is not saved. A Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is created, the project is automatically saved each time a change is made.
Structures can be imported from the PDB directly, or from your Working Directory using File > Import Structures , and are added to the Entry List and Project Table. The Entry List is located to the left of the Workspace . The Project Table can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.
1. Double click the Maestro icon to start Maestro
○ (No icon? See Starting Maestro ) 2. In a browser, go to http://bit.ly/2xtMuOx
to download the required tutorial files
Figure 2-1. Change Working Directory option.
3. Go to File > Change Working Directory 4. Navigate to your chosen directory and
click Choose 5. Copy the downloaded tutorial files to
your Working Directory 6. Unzip the tutorial file
1
Figure 2-2. Open Project panel.
7. Go to File > Open Project 8. Select the file Torsional
Scanning.prjzip 9. Click Open
○ Structures are shown in the Entry List
○ A structure is included in the Workspace
Note: Please see the Glossary of Terms for the distinction between included and selected.
Figure 2-3. Warning box to save scratch project.
10. In the Save scratch project warning box, click OK
Figure 2-4. Save Project panel.
11.Go to File > Save Project As 12.Change the File name to
MM_Confgen_tutorial 13.Click Save
○ The project is named MM_Confgen_tutorial.prj
2
3. Scanning Torsions and Understanding Barriers In this sections, we will use MacroModel Coordinate Scan to setup and analyze simple torsions of a single compound to gain a better understanding of the energetic barriers of a small molecule. We will superimpose the output conformations to a common core, for easier visualization. Next, we will use the potential energy surface to find low energy conformations of a small molecule. The potential energy surface of a compound can help with understanding key aspects of a molecule's behavior. This gives us an indication of how adaptable the molecule is and how much strain is needed for it to adopt a particular conformation. These steps are a prelude to a full conformational search, which can explore many torsions of a small molecule simultaneously or systematically. We will use the potential energy surface to find low energy conformations of a small molecule.
3.1 Set up a torsional scan
Figure 3-1. Select all entries in Ddrive and include the first entry.
1. In the Entry List, select and expand the group Ddrive
○ All entries are selected 2. Include the Ddrive_starting structure
○ The structure, labeled by atom numbers, is in the Workspace
Note: You can apply atom number labels in the Style toolbox by clicking the Apply Labels arrow and choosing Element + Atom Number
Figure 3-2. Coordinate Scan in MacroModel.
3. Go to Tasks > Browse > MacroModel > Coordinate Scan
○ The Coordinate Scan panel opens
3
Figure 3-3. Choose Dihedral as Coordinate Type.
4. For Use structures from, choose Workspace (included entry)
5. Click the Scan tab 6. For Coordinate Type, choose Dihedral
Figure 3-4. Select dihedrals in the Workspace.
7. In the Workspace , select atom numbers 1 , 14 , 15 , and 16
○ Atoms are highlighted ○ Torsion 1 is defined
8. Select atom numbers 1 , 6 , 25 , and 26 ○ Torsion 2 is defined
4
Figure 3-5. Set solvent to ‘none’ for gas phase.
9. In the Coordinate Scan panel, click the Potential tab
10.For Solvent, choose None ○ A gas phase minimization will be
run 11.For Job name, type mmod_Ddrive 12.Click Run
○ This job takes ~2 minutes to complete on 1 CPU
○ To save time, we will look at pregenerated results
3.2 Analyze torsional scan results
Figure 3-6. Include the lowest energy structure found and display properties in the Entry List.
1. In the Entry List, click the Settings button (cog)
2. Choose Show Property
Figure 3-7. Show the Potential Energy property.
3. For Subset, choose MacroModel All 4. Click Potential Energy-OPLS3 kcal/mol 5. Click OK
○ The Potential Energy property is shown in the Entry List
○ Widen the Entry List, if needed Note: The Potential Energy-OPLS3 property is given in kJ/mol
5
Figure 3-8. Potential and Relative Energy properties, shown in kcal/mol.
6. Repeat steps 4 and 5, choose Relative Energy-OPLS3 kcal/mol
7. Click OK ○ The Relative Energy property is
shown in the Entry List Note: The last entry in the Ddrive group is the lowest energy structure found from scanning the two dihedrals
Figure 3-9. Superposition option in Structure Alignment.
8. Go to Tasks > Browse > Structure
Alignment > Superimposition ○ The Superposition panel opens
Figure 3-10. Superimpose by selected entries.
9. Under Entries to superimpose, choose Selected Entries
10.Click the SMARTS tab
6
Figure 3-11. Select the pyrimidine core.
13.Type A ○ Atom pick mode is activated
14. In the Workspace , use shift-click to select the pyrimidine core
15. In the Superposition panel, click Get from Selection
○ The selected structures are aligned to the pyrimidine core
○ RSMDs for the structures are shown in the bottom of the panel
Figure 3-12. Fix the starting structure and toggle through the results.
16. In the Entry List, double-click the In circle next to Ddrive_starting structure
○ The structure is fixed in the Workspace
17. Include the second entry 18.Use the left and right arrow keys to
step through the conformations
Figure 3-13. Include multiple entries in the Workspace.
Note: Use shift-click to include contiguous entries or ctrl-click (cmd-click) in include non-contiguous entries in the Workspace
7
3.3 View the potential energy surface
Figure 3-14. Plot Two Coordinate Scan option in MacroModel.
1. Go to Tasks > Browse > MacroModel > Plot Two Coordinate Scan
○ The Plot of Two-Coordinate Scan panel opens
Figure 3-15. Open the coordinate scan output.
2. At the bottom left of the panel, click Open
3. Double-click Ddrive and choose Ddrive-out.grd
4. Click Open ○ The potential energy landscape is
shown, colored rainbow ○ Low energies are shown in blue,
high energies are shown in red
Figure 3-16. The Plot of Two-Coordinate Scan panel using kcal/mol energy units.
5. Under Energy units, choose kcal/mol 6. Ensure that the Energy scale is set to
Absolute ○ Min Energy 12.5 Kcal/mol (shown
by blue green contour lines) ○ Max energy 34.9 Kcal/mol (shown
by yellow red contour lines) Note: The energy scale is absolute because we are only studying a single molecule, rather than comparing several molecules
8
Figure 3-17. Analysis of the potential energy plot of the Ddrive molecule.
Note: This plot shows there are large patches of lower energy with relatively sparse contour spacing between them. This suggests a reasonable freedom of movement of the two torsions relative to each other. However, when Torsion 2 lies close to 360/0°, no angle of Torsion 1 is tolerated well.
Figure 3-18. Apply CPK representation to the starting and lowest energy structures.
7. In the Entry List, double-click the In circle next to Ddrive_starting structure
○ The structure is no longer fixed in the Workspace
8. Ctrl-click (Cmd-click) to include the last two entries in the group
9. Ctrl-click (Cmd-click) to include the last two entries in the group
10.Click Style and choose Apply CPK representation
Figure 3-19. Tiled view of a low and high energy conformation, showing a steric clash.
11.Type Ctrl-L (cmd-L) ○ The Workspace is tiled ○ The steric clash between the CH 2
group and phenyl ring can be visualized
12.Type Ctrl-L (cmd-L) ○ The Workspace is un-tiled
13.Right-click empty Workspace and choose Clear Workspace
9
Figure 3-20. Toggle properties on and off with the Property Tree.
Note: Looking into the energetic components of the system can help explain a potential energy surface.
14.Type ctrl-T (cmd-T) ○ The Project Table opens
15.Click Tree to open the Property Tree ○ Different calculated properties can
be toggled on and off ○ Click the arrow next to each
application to view more properties
16.Double-click All ○ All the properties are hidden
17.Open the tree to MacroModel > Secondary
18.Under Secondary, check Bend Energy - OPLS3 kcal/mol and Van der Waal Energy - OPLS3 kcal/mol
○ The Project Table is updated with the chosen properties
Note: There is a high VdW energy between the phenyl group and the nearby CH 2 group of Torsion 1. This causes the pyrimidine core to distort and result in a high energy bend.
4. Scanning Torsions for a Series of Molecules As part of a medicinal chemistry exploration project, it is often helpful to change a single-atom linker in a molecule to evaluate the impact it has. We will change the linker atom in a series of molecules and analyze the torsions to control the shapes of molecules of interest. Additionally, we will use the Protein-Ligand Database (PLDB) to examine the statistics of these types of torsions in similar molecules in the PDB. For more information on using the PLDB, please see the Protein-Ligand Database Tutorial . Please note that you will need a license for the PLDB to follow this section of the tutorial.
10
4.1 Set up the scans
Figure 4-1. Include the first entry of the Phenyl-linker-Pyridyl group.
1. In the Entry List, expand and select the group Phenyl-linker-Pyridyl
2. Include the first entry, Ph-O-Py 3. Go to Tasks > Browse > MacroModel >
Coordinate Scan ○ The Coordinate Scan panel opens
Figure 4-2. Set the two dihedral angles.
4. For Use structures from, choose Workspace (included entry)
5. Click the Scan tab 6. For Coordinate Type, choose Dihedral 7. In the Workspace , select atom numbers
3 , 2 , 12 , and 15 ○ Atoms are highlighted ○ Torsion 1 is defined
8. In the Workspace , select atom numbers 14 , 15 , 12 , and 2
○ Torsion 2 is defined
11
Figure 4-3. Set solvent to ‘none’ for gas phase.
9. In the Coordinate Scan panel, click the Potential tab
10.Under Solvent, choose None ○ A gas phase minimization will be
run 11.Next to Job name, type drive_PhOpy 12.Click Run
○ This job takes ~10 minutes to complete on 1 CPU
○ To save time, we will look at pregenerated results in the next section
Figure 4-4. Repeat the coordinate scan setup for the series of molecules.
13. In the Entry List, include Ph-S-Py ○ The linker is now a sulfur atom ○ C-S has a greater bond length
14.Repeat steps 5-12, naming the job drive_PhSpy
15.Repeat steps 13-14 for Ph-CH2-Py and Ph-NH2-Py , changing job names
○ These jobs take ~10 minutes each to complete on 1 CPU
○ To save time, we will look at pregenerated results
Note: Ensure that atoms are chosen in the same order across all calculations. Reversing the order will make interpreting the results nonsensical. Keep torsion 1 and torsion 2 equivalent across the series.
12
4.2 Analyze the results of the linker series
Figure 4-5. Filter the Entry List.
1. In the Entry List, click the Search magnifying glass
2. Type Minimum 3. Click the arrow next to each filtered
group to expand ○ Only the entry with the minimum
energy is shown 4. Shift-click to include all four minimum
energy entries
Figure 4-6. Tile view of the four energy minimized conformations.
5. Type Ctrl-L (Cmd-L) ○ The Workspace is tiled
6. Type Ctrl-Y (Cmd-Y) ○ The Preset rendering is applied
7. Go to Tasks > Browse > Structure Alignment > Superimposition
○ The Superposition panel opens 8. Under Entries to superimpose, choose
Included entries 9. Click the SMARTS tab 10. In the Workspace , use shift-click to
select a pyridine 11. In the Superposition panel, click Get
from Selection 12.Type Ctrl-L (Cmd-L)
13
Figure 4-7. Superimpose included entries by SMARTS.
○ The Workspace is un-tiled
Figure 4-8. The lowest energy conformations of the linker series compounds.
As seen in Figure 4-8, changing the linker from an oxygen (in the structure with grey carbons) to a sulfur (in the structure with green carbons), alters the phenyl ring orientation with respect to the pyridyl nitrogen. The CH 2 linker induces the least planar conformation, due to sterics, while the NH 2 linker is most coplanar with the pyridyl ring.
4.3 Examine predicted torsions against PLDB data (optional)
Figure 4-9. Clear the Entry List filter.
1. Click the X to clear the Entry List filter 2. Include 1XLS (unprepared) 3. Type L
○ The Workspace is zoomed to the ligand
Figure 4-10. The bound ligand agrees with predicted lowest energy O-linked conformation.
Note: The orientation of the bound ligand around the O-linker agrees with the lowest energy conformational result for the O-linked compound in section 4.2 .
14
Figure 4-11. The bound ligand conformation is influenced by the CF 3 group.
4. Include 2WAP (unprepared) 5. Type L
○ The Workspace is zoomed to the ligand
Note: The orientation of the bound ligand around the O-linker is ~180° different from the lowest energy conformational result for the O-linked compound in section 4.2. The strongly electron-withdrawing CF 3 group on the bound ligand has weakened the conformational preference of the lone pair electrons on the oxygen linker.
Figure 4-12. PLDB Search option in Structure Analysis.
6. Go to Tasks > Browse > Structure Analysis > PLDB Search
○ The Connect to PLDB Search panel opens
7. Enter your Server URL, User Name, and Password
8. Click Log In ○ The PLDB Search panel opens
Note: You must have a PLDB license to do these steps.
Figure 4-13. Open a new search in PLDB.
9. Click New Search ○ The PLDB Search - Sketcher
opens
15
Figure 4-14. Draw the N-linked series compound.
10. In the Sketcher, draw the PhNH2Py structure from section 4.1
Figure 4-15. Select the first torsion.
11.Click Torsion 12.Click on each atom in the first NH 2 linker
torsion to make the torsion measurement
Figure 4-16. Input torsion limits for the search.
13. In the Input torsion limits panel, next to Is between, type 0 and 360
14.Click Ok ○ The torsion search is highlighted in
green
16
Figure 4-17. Select the second torsion.
15.Repeat steps 39-41 for the second NH2 linker torsion
Figure 4-18. Start PLDB search.
16.Click Start Search ○ This search takes ~1 minute ○ Results are shown in the PLDB
Search panel
Figure 4-19. View PLDB search results.
17.Click View Results (61)
17
Figure 4-20. Scatter plot of the search results.
18.Click Show Plots/Hide Plots 19.Choose the Scatter Plot tab
○ Two conformations are preferred in the literature
○ The two low energy conformations are ~180° different
20.Close the PLDB Search Results and PLDB Search panels
5. Generating Small Molecule Conformers MacroModel is an engine for conformational searching, with substantial options for controlling solvents, force fields, constraints, and settings associated with navigating a potential energy surface. In this section, we will explore how the choice of solvent affects the conformations that can be found for a small peptide, KFGLE. This peptide has been designed to allow the possibility of a salt bridge interaction between the side chains of the terminal lysine and glutamic acid residues. We will compare different searching methods, observing that some that allow this interaction to dominate, and others do not. This highlights how the solvent environment of a system is an important consideration for obtaining a meaningful set of conformers.
5.1 Set up conformational searches
Figure 5-1. Open ConformationsPeptide project.
1. Go to File > Open Project 2. Choose the file
ConformationsPeptide.prjzip 3. Click Open
○ Structures are shown in the Entry List
○ The KFGLE structure is included in the Workspace
4. In the Save scratch project warning box, click OK
18
Figure 5-2. Save project as MM_peptide.
5. Go to File > Save Project As 6. Change the File name to MM_peptide 7. Click Save
○ The project is named MM_peptide.prj
○ Entry KFGLE is included
Figure 5-3. Conformational Search option in MacroModel.
8. Go to Tasks > Browse > MacroModel > Conformational Search
○ The Conformational Search panel opens
Figure 5-4. Potential tab in Conformational Search.
9. For Use structures from, choose Workspace (included entries)
10. In the Potential tab, for Solvent, choose Water
19
Figure 5-5. Mini tab in Conformational Search.
11.Click the Mini tab 12.For Maximum iterations, type 2000 13.For Job name, type
peptide_cs_2000it_water 14.Click Run
○ This job will take 10-15 minutes to complete on 1 CPU
○ To save time, we will look at pregenerated results
15.Repeat steps 10-14, choosing CHCl3 as the solvent and naming the job peptide_cs_2000it_chcl3
○ This job will take 10-15 minutes to complete on 1 CPU
○ To save time, we will look at pregenerated results
Figure 5-6. Bioactive Search option in Structure Analysis.
16.Go to Tasks > Browse > Structure Analysis > Bioactive Search
○ The ConfGen panel opens
20
Figure 5-7. ConfGen panel.
17.For Use structures from, choose Workspace (1 included entry)
18.For Target number of conformations, type 50
19.Change the Job name to KFGLE_ConfGen
20.Click Run ○ This job will take ~5 minutes to
complete on 1 CPU ○ To save time, we will look at
pregenerated results
5.2 Analyze and compare the conformational search results
Figure 5-8. Include the results in the Workspace.
1. In the Entry List, right-click the group peptide_cs_2000it_water-out
2. Choose Include 3. In the Warning box, click Continue
○ The structures are included in the Workspace
4. Ctrl-click (Cmd-click) to exclude KFGLE
Figure 5-9. The Interactions panel.
5. In the Workspace Configuration Toolbar, right-click Interactions
○ Interactions panel opens 6. Next to Non-covalent bonds, choose
Intra-Ligand 7. Under Contacts/Clashes, turn off Bad
and Ugly
21
Figure 5-10. Intramolecular interactions of the peptide conformations generated in water.
Note: The intramolecular hydrogen bonds and salt bridge of the conformations generated in water align well.
8. In the Entry List, right-click peptide_cs_2000it_water-out
9. Choose Exclude ○ The structures are removed from
the Workspace
Figure 5-11. Intramolecular interactions of the peptide conformations generated in chloroform.
10. In the Entry List, right-click on the group peptide_cs_2000it_chcl3-out
11.Choose Include 12. In the Warning box, click Continue
○ The structures are included in the Workspace
Note: The are more intramolecular interactions when the peptide is modeled in chloroform, as compared to water.
22
Figure 5-12. The Property Table with only AromaticBond, Halogen, HBond and SaltBridge added.
13.Type Ctrl-T (Cmd-T) ○ The Project Table opens
14.Click the Property Tree button ○ The Property Tree appears on the
right of the Project Table 15.Click the All box twice
○ All boxes are deselected 16.Next to Maestro, click the arrow 17.Check AromaticHBond, Halogen,
HBond, and SaltBridge ○ These properties are shown in the
Project Table
23
Figure 5-13. The Calculate Properties panel.
19.Select both the water and chloroform output groups
20. In the Project Table, go to Data > Add Property > Standard Molecular Property
○ The Calculate Properties panel opens
21.Select Number of h-bonds and halogen bonds and Number of Pi interactions with Ctrl-click
22.Click on Selected Entries ○ This updates the Project Table
with new columns containing the values for all selected rows
24
Figure 5-14. View of the Entry List with the selected results and the first entry included.
23.Right-click in the Workspace and select Clear Workspace
24.Click on the KFGLE_ConfGen group header to select the whole group
25. Include the first entry in the Workspace
Figure 5-15. Measuring a distance in one conformation and applying it to all selected entries.
26.On the Favorites toolbar, click Measure 27. In the banner that opens, set Measure to
Distance Define the measurement of the terminal residues, K and E
28.Pick atoms 6 and 77 in the Workspace ○ This measures the distance for a
single molecule 29.Right-click the distance label in the
Workspace 30.Select Calculate Property…
○ This opens the Calculate Measurements Property window
25
Figure 5-16. The Project Table showing the newly added column (highlighted in red) for the Distance property calculated for all conformations.
31.Define a new Property name or keep the default; click OK
○ This creates a new column in the Project Table. By default, it is named Distance atom number - atom number
Figure 5-17. Results of Entry ID vs Distance to show distribution of extended conformations coming from ConfGen (top) and non-extended conformations coming from MacroModel -water solvent model (bottom) .
Note: Plots have been pregenerated for easy viewing
32.Click the Plot icon in the Project Table ○ The Manage Plots panel opens
and there are two scatter plots that are already present and named
33.Click on each of the Plots to view them (figure 4-13)
Note: You can also create new plots from scratch in the Manage Plots panel
34.Choose New scatter plot ○ An empty Scatter Plot opens as a
new Window 35.Define the X axis as Entry ID and Y axis
as Distance to generate a new scatter plot
26
5.3 Build a peptide (optional)
Figure 5-19. Open Build Peptide from Sequence panel.
1. Click Build
○ The 3D Builder panel opens 2. Click Other Edits and choose Build
Peptide from sequence ○ The Build Peptide From Sequence
panel opens
Figure 5-20. Build Peptide From Sequence panel.
3. For Title, write KFGLE 4. For Sequences, write KFGLE 5. For Shape, choose Structure: Extended 6. Click Build
○ A peptide with the specified sequence and secondary structure has been added to the Entry List
6. Optimizing Conformations with Mogul Mogul is a program that can be used to validate molecular geometries, as it contains precise information on preferred molecular geometries through access to millions of chemically classified parameters derived from the CSD. It is set up to check on bond lengths, valence angles, acyclic torsion angles, and ring conformations, and such searches are directly accessible through Maestro, under Tasks. This is, however, a license-based tool from CCDC and requires configuration to set up. Please see Configuring Mogul for Maestro Use for instructions.
27
Figure 6-1. Finding CSD panels in Tasks
1. Click Tasks , type Mogul and press Enter
2. Click CSD Search ○ The Query Cambridge Structural
Database panel opens
Figure 6-2. The Query CSD panel.
3. Include the first entry from the ConfGen group
4. Under Query CSD with ligand from, select Workspace
5. Under Search fragments, choose All torsions
6. Click Run ○ This job should take ~10 minute to
complete 7. When the job finishes, click incorporate
in the banner
28
Figure 6-4. The offensive torsion C77-C80 with a value of 12.31 is shown in red in the Workspace and in the Analysis Panel
8. Click Tasks , type Mogul and click Enter 9. Click CSD Analysis
○ Each torsion is shown qualitatively (green = ok and red = bad), and is interactive with the Workspace
○ Torsion C77-C80 is outside the range of where other torsion hits are found in the CSD. Ideally, it should lie between 40 and 80 degrees and 160-180 degrees
Figure 6-5. A histogram showing torsion C77-C80 (red line) to be outside the distributions of torsion hits found in the CSD (green bars).
11.Click on the torsion, C77-C80 ○ A histogram is displayed showing
the distribution of the torsion hits found in the CSD
Note: For more details on Mogul, please refer to the link here
12.Go to File > Close Project
7. Clustering Methods In Maestro, we can cluster by conformations using torsions or atomic positions, which we will explore here.
1. Go to File > Open Project 2. Select Torsional Scanning.prjzip and
click Open ○ Structures are shown in the Entry
List
29
Figure 7-1. Select all entries in Ddrive and include the first entry.
3. Select and expand the group Ddrive ○ All entries are selected
4. Include the Ddrive_starting structure ○ The structure, labeled by atom
numbers, is in the Workspace
Figure 7-2. Using the Tasks search to find the Clustering of Conformers option.
5. Click Tasks , search for Cluster and press Enter
6. Select Clustering of Conformers ○ The Conformer Cluster panel
opens
Figure 7-3. The Conformer Cluster panel.
7. For Use structures from, choose Project Table (1371 selected entries)
8. For Generate RMSD Matrix, choose Atomic RMSD
9. For Define comparison atoms, click Heavy atoms
○ The heavy atoms are listed in the window above
10.For Linkage method, choose Average 11.For Number of clusters to generate, type
100 12.For Incorporation, choose One structure
(nearest to centroid) per cluster 13.Change the Job name to
conf_cluster_atom 13.Click Run
○ This job takes about 3-4 minutes to complete
30
Figure 7-4. The Clustering Statistics panel.
14.Click Clustering Statistics ○ The Clustering Statistics panel
opens 15.Under Plot, choose Kelley Penalty from
the Plot menu and observe the plot ○ In this case around 53 clusters are
ideal as the penalty is at its the lowest. This can be seen by hovering on the plot in that area, which updates the x and y-variable value at the top-right hand side of the panel
Note: Clicking in the plot sets the number of clusters in the Conformer Cluster panel
8. Conclusions and References MacroModel is a powerful tool to explore the full range of conformations for small molecules, and has can also be used to analyze protein-ligand complexes. We have examined how specific settings can make a difference to the conformational output, so understanding the choices you make are important to the results. Through the exploration of small molecules, we observed how conformations can vary due to a single atom change and how this information can be used in lead optimization. For further information, please see: Macromodel User Manual Protein-Ligand Database Tutorial
9. Glossary of Terms Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
included - the entry is represented in the Workspace, the circle in the In column is blue
incorporated - once a job is finished, output files from the Working directory are added to the project and shown in the Entry List and Project Table
Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data
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Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project
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
Working Directory - the location that files are saved
Workspace - the 3D display area in the center of the main window, where molecular structures are displayed
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