Desmond Tutorial

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<strong>Desmond</strong> <strong>Tutorial</strong> Preparing Proteins with Missing Residues or Side Chains Figure 3.4 Input Sequence From File window in Prime Navigate your hard drive and select the original PDB file. Click the ‘Read’ button. NOTE c. Navigate your directory structure and select the original 1su4 PDB file from the Files area of the window, then click Read. The full sequence (994 residues) is read from the SEQRES fields and can be seen at the top of the Structure Prediction window as shown in Figure 3.5. Reading in the sequence from a PDB file is generally not a good idea. Often a few residues are missing in the protein structure from either or both termini. Since we do not want Prime to build the head or tail of the structure, we need to truncate the sequence by hand, editing the SEQRES fields to ensure that the SEQRES fields start at column 20 in the PDB file and have a total of 13 residues (except for the last field). The number of residues should also be decreased accordingly. Since, however, Prime can read all kinds of protein sequence file formats (FASTA, NEXUS, and so on), you should use one of these formats. 32 D. E. Shaw Research September 2008
Preparing Proteins with Missing Residues or Side Chains Running Prime Figure 3.5 Full sequence in the Prime Structure Prediction window The full sequence of 994 residues appears at the top of the window. Click Next. d. When you are finished reading the input sequence, click Next. At this point Find Homologs is highlighted in the workflow diagram (the Guide) at the bottom of the window as shown in Figure 3.6. September 2008 D. E. Shaw Research 33
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 and 16: Desmond Tutorial Tutorial Steps Fig
Page 17 and 18: Desmond Tutorial Tutorial Steps 3.
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: Preparing Proteins with Missing Res
Page 47 and 48: Preparing Proteins with Missing Res
Page 55 and 56: 4 Preparing a Desmond simulation wi
Page 57 and 58: Preparing a Desmond simulation with
Page 69 and 70: 5 Finishing Preparations for Desmon
Page 71 and 72: Finishing Preparations for Desmond
Page 77 and 78: 6 Running Desmond Simulations Overv
Page 79 and 80: Running Desmond Simulations Running
Page 81 and 82: 7 Preparing Free Energy Perturbatio
Page 83 and 84: Preparing Free Energy Perturbation
Page 93 and 94: 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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Desmond Tutorial

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