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Ligand FEP Tutorial - Schrödinger Flipbook PDF
ga P Toa Page 1 of 5 Ligand FEP Tutorial Created August 2015 with Release 15-3 This tutorial demonstrates all the ...
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August 2015
MOLECULAR DYNAMICS
Ligand FEP Tutorial Created August 2015 with Release 15-3 This tutorial demonstrates all the steps neccesary to set up and analyze a single Free Energy Perturbation (FEP) between two ligands using Ligand FEP. The tutorial consists of three parts.
1. Preparation 2. Ligand FEP Setup 3. Ligand FEP Analysis Required Files: Ligand_FEP_Tutorial.zip
Download: http://www.schrodinger.com/tutorials/Ligand_FEP_Tutorial.zip
1: Preparation: Importing and preparing your protein from PDB For more details and examples of protein preparation, see Chapter 2. Preparing Proteins in the Desmond Quick Start Guide. In this tutorial, you will import the protein structure 4DJV (β-secretase-1 or BACE-1) from the PDB, containing ligand 4b from reference [1] and prepare it for Ligand FEP. A prepared complex structure has been provided (4DJV_complex.mae). 1. Choose Tasks → Protein Preparation or click the Prep Wiz toolbar button. 2. Enter 4DJV into the textbox, check Biological unit, and click Import.
Figure 1. Protein Preparation Wizard panel. Here, we check Biological unit to only include the monomer. The PDB file will be automatically downloaded into your working directory and imported into Maestro.
1 Cumming, Jared N., et al. “Structure based design of iminohydantoin BACE1 inhibitors: identification of an orally available, centrally active BACE1 inhibitor.” Bioorganic & medicinal chemistry letters 22.7 (2012): 2444-2449
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3. Ensure the boxes in FIgure 2 are checked and click Preprocess.
Figure 2. Protein Preparation Wizard, Import and Process tab. The processed protein structure will automatically be incorporated into the Workspace and a new entry will be created in the Entry list, below your unprocessed entry. Optional: Fill in missing side chains and loops. (Requires Prime license).
4. Under the Refine tab, in the H-bond assignment section, click Optimize.
Figure 3. Protein Preparation Wizard, Refine tab. Suggested: Click Remove waters with less than N H-bonds to nonwaters. Suggested:Under the restrained minimization section, click Minimize.
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5. Right click your processed entry in the Entry List and choose Split → Into Ligands, Water, Other.
Figure 4. Prepared entries in the Entry List. Optional: Remaining waters are likely important and should be kept. In this tutorial, we will keep the waters entry. Otherwise, to delete crystallographic waters simply delete the 4DJV_waters entry.
6. 4DJV_ligand1 is our ligand of interest. Merge the remaining entries (ligand 2, waters, and protein) by selecting them, right clicking, and then choosing Merge. 7. Select 4DJV_ligand1 and your merged entry, right click, and choose Group → New… 8. Select the row containing your group and click the Export panel button to save your prepared structure. You can do this at any time to save your progress.
2. Ligand FEP Setup For every ligand in your desired FEP calculations, you must minimize the core RMSD by either (A) manually building the ligand from a duplicated entry or (B) superimposing an imported ligand file. For this tutorial, option (A) will be followed. We will create the ligand found in PDB 4DJY, containing ligand 24 from reference [1] using ligand 4b as the core. A prepared file for Ligand FEP has been provided (4DJV_LigFEP.mae). 1. Right click the ligand1 entry and select Duplicate → In Place 2. Introduce the appropriate mutations to the new ligand entry by using the Build or Fragments Toolbar. The mutations for this tutorial are highlighted in red in Figure 6 below. a. Click the arrow next to the Delete button and choose Atoms, then click on the carbon atoms in the ring on the left, leaving the one that is joined to the rest of the molecule. b. Click the cyclopropyl button, then click on the carbon atom that you didn’t delete from the ring. c. Right-click on the oxygen of the methoxy group and choose Set Element → C. d. Click the Increment bond order button, then click twice on the bond from the atom you just changed to the methyl group.
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e. Click the arrow next to the Select button and choose Atoms, then drag over the acetylene unit to select the two carbons and the terminal hydrogen. f. Press CTRL + M.
Figure 5. Build (left) and Fragments (right) toolbars.
4. Open the Ligand FEP Panel by choosing Tasks → Molecular Dynamics → Ligand FEP...
Figure 6. Ligand FEP Panel. The mutations needed for this tutorial are highlighted in red.
5. Import your ligands and protein by selecting the group containing your ligands and protein in the Entry List or Project Table and then choosing to import from the Project Table. 6. Check that the two desired ligands for your FEP calculation have been added to the panel. If you’ve imported more than two ligands you can select the ones you are interested by using the drop down menu above each ligand.
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7. Ensure you have correctly set up the desired mutation by checking the several viewable atom properties: • Mutation: highlights the fragments or atoms that are being changed in RED • Atom mapping: shows the atom numbering of the common core • Common core: highlights the common atoms in GREEN • Hot atoms: highlights the atoms involved in the alchemical transformation in ORANGE 8. Submit your run with the desired job settings or write out your input files for upload to your cluster. Input files for the job have also been provided (set up to run on GPU).
3. Ligand FEP Analysis The .sid and .cms files for analysis and the output FEP reports/simulation interaction diagrams have also been provided for this tutorial. The experimental ΔΔG for ligand 4b to ligand 24 is -2.15 kcal/mol. The results in this tutorial yield a ΔΔG of -1.42 kcal/mol. 1. Extract the tar file from the final step of the complex and solvent calculations. Located in /_fep1/_2/_complex_12-out.tgz /_fep1/_2/_solvent_13-out.tgz 2. Locate the .sid file in the extracted results. _complex_10.sid ; _solvent_11.sid 3. Generate a PDF FEP report on both the complex and solvent calculations by: ► $SCHRODINGER/run -FROM desmond fmapper_sid2pdf.py -cms • Report contains information regarding: simulation details, protein & ligand information, the ΔΔG corresponding to the leg, convergence & overlap, and replica exchange monitor. 4. Generate the Simulation Interaction Diagram: run parse_sid.py to generate .eaf files. ► $SCHRODINGER/run parse_sid.py 5. View the Simulation Interaction Diagram with the command: ► $SCHRODINGER/run event_analysis.py
Additional Resources • •
For more information and examples using Desmond MD please see the Desmond Quick Start Guide and Desmond User Manual included in the Documentation. For additional support and to communicate with other users please visit the Desmond MD User’s Google Group: https://groups.google.com/forum/#!forum/desmond-md-users
Acknowledgements •
Schrödinger would like to thank Nathan Lim for his work creating this tutorial.
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