SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 3)

CONTENTS 3

Contents

1 Building a Structural Model of KcsA 7

1.1 Downloading and Viewing the Protein . . . . . . . . . . . . . . . 7

1.2 Examining the PDB File . . . . . . . . . . . . . . . . . . . . . . . 9

1.3 Building the KcsA Tetramer . . . . . . . . . . . . . . . . . . . . . 10

1.4 Generating PSF and PDB Files for KcsA . . . . . . . . . . . . . 13

1.5 Solvating the Protein (Optional) . . . . . . . . . . . . . . . . . . 19

2 Placing KcsA in a Membrane 25

2.1 Building a Membrane Patch . . . . . . . . . . . . . . . . . . . . . 25

2.2 Alignment of Membrane and Protein . . . . . . . . . . . . . . . . 26

2.3 Combination of Membrane and Protein . . . . . . . . . . . . . . 27

2.4 Solvation and Ionization . . . . . . . . . . . . . . . . . . . . . . . 30

3 Running a Simulation of KcsA 35

3.1 Melting of Lipid Tails . . . . . . . . . . . . . . . . . . . . . . . . 35

3.2 Minimization and Equilibration with Protein Constrained . . . . 40

3.3 Equilibration with Protein Released . . . . . . . . . . . . . . . . 42

3.4 Production Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

1 2 3 4 5 6 7 8 ... 42 43

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SanDisk Membrain Software Manual do Utilizador Página 3