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| - | {{EPF-Lausanne09}}
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| - | <div CLASS="epfltrick">__TOC__
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| - | </div><div CLASS="epfl09">
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| - | We start with the PDB file of the protein, obtained through the Protein Data Bank.
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| - | 1. We open VMD, and lauch our protein
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| - | 2. Creation of the pdb file
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| - | In the Tk Console menu of VMD we open the VMD TkCon window, and type the following commands:
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| - | : set our_protein [atomselect top not water and not GOL]
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| - | : $our_protein writepdb our_protein.pdb
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| - | This will select all the protein except the water and except the glycerol, with the cofactor.
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| - | We have created the file our_protein.pdb, which contains the coordinates of the protein alone without hydrogens.
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| - | Quit VMD.
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| - | 3. Creation of the psf file
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| - | There is 2 ways to create a psf:
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| - | * in VCMD, Extensions → Modeling → Automatic PSF Builder
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| - | * We first make a pgn file, which will be the target of psfgen.
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| - | In a Terminal window, open a text editor and type:
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| - | : package require psfgen
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| - | : topology top all27 prot lipid.inp
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| - | : pdbalias residue HIS HSE
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| - | : pdbalias atom ILE CD1 CD
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| - | : segment U
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| - | : {pdb ubqp.pdb}
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| - | : coordpdb ubqp.pdb U
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| - | : guesscoord
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| - | : writepdb ubq.pdb
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| - | : writepsf ubq.psf
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| - | In a Terminal window, type the following command:
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| - | > vmd -dispdev text -e our_protein.pgn
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| - | This will run the package psfgen on the file ubq.pgn and generate the psf and the pdb file of ubiquitin with hydrogens.
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| - | A new pdb file with the complete coordinates of all atoms is written, including H; and a psf file with the complete structural information of the protein.
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| - | 4. Solvating the Protein
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| - | Now, the protein needs to be solvated, i.e., put inside water, to more closely resemble the cellular environment. This will be done by placing the protein in a water box, in preparation for minimization and equilibration with periodic boundary conditions.
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| - | In the VMD Main window, open the Tk Console, and type:
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| - | : package require solvate
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| - | : solvate our_protein.psf our_protein.pdb -t 5 -o our_prot_in_a_water_box
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| - | </div><div CLASS="epfl09bouchon"></div>
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