Desmond Tutorial

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Desmond Tutorial Desmond Tutorial Figure 1.2 Maestro main window Select Project > Import Structures Maestro workspace 2. Import a protein structure file into your workspace by selecting Project > Import Structures from the menu bar. The Import panel appears as shown in Figure 1.3. Figure 1.3 Import panel Select ‘PDB’ from the ‘Format’ field. Click the ‘Get PDB File’ button. 4 D. E. Shaw Research September 2008
Desmond Tutorial Tutorial Steps 3. Select the type of structure file you will import from the Format field. For this tutorial, select PDB because we will import a PDB (Protein Databank File). NOTE Maestro supports many common file formats for structural input. See the Maestro tutorial (Section 11) or click the Help button for a list of supported formats. 4. Click the Get PDB File button. The Get PDB File window appears as shown in Figure 1.4. Figure 1.4 Get PDB File window Enter the identifier for the PDB file you want to import in the ‘PDB ID’ field. Check the ‘Download from Web’ option. Click the Download button. 5. Enter the identifier for the PDB file you want to import into the PDB ID field. For this example, we will import the small, proteinase (trypsin) inhibitor protein: 4pti. Therefore, enter 4pti in the PDB ID field. 6. Check the Download from Web option to allow Maestro to download the PDB file from the PDB website. 7. Click the Download button. The protein structure appears in the Maestro workspace as shown in Figure 1.5. The protein structure is displayed using a ribbon representation with colors continuously varying along the rainbow scale from the N terminus toward the C terminus. The red dots show the location of the oxygen atoms of the water molecules present in the X‐ray structure. September 2008 D. E. Shaw Research 5
Page 1 and 2: Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
Page 5 and 6: from outermost to innermost, separa
Page 7 and 8: Contents Preface . . . . . . . . .
Page 9 and 10: Loading Files from the Command Line
Page 11 and 12: List of Figures Figure 1.1: Simulat
Page 13 and 14: 1 Desmond Tutorial Introducing Desm
Page 15: Desmond Tutorial Tutorial Steps Fig
Page 19 and 20: Desmond Tutorial Tutorial Steps Fig
Page 21 and 22: Desmond Tutorial Tutorial Steps 11.
Page 25 and 26: Desmond Tutorial Tutorial Steps 18.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
Page 31 and 32: 2 Learning the Maestro- Desmond Env
Page 33 and 34: Learning the Maestro-Desmond Enviro
Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
Page 55 and 56: 4 Preparing a Desmond simulation wi
Page 57 and 58: Preparing a Desmond simulation with
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Preparing a Desmond simulation with
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5 Finishing Preparations for Desmon
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Finishing Preparations for Desmond
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6 Running Desmond Simulations Overv
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Running Desmond Simulations Running
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7 Preparing Free Energy Perturbatio
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Preparing Free Energy Perturbation
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8 Visualization and Analysis using
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Visualization and Analysis using Ma
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9 Analyzing Trajectories Using VMD
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Analyzing Trajectories Using VMD Lo
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD An
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Analyzing Trajectories Using VMD Bi
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10 Documentation Resources Detailed
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