From 2009.igem.org
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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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| - | <br>set our_protein [atomselect top not water and not GOL]
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| - | <br>$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 ο¬le 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 β Modeling β 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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| - | <br>package require psfgen
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| - | <br>topology top all27 prot lipid.inp
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| - | <br>pdbalias residue HIS HSE
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| - | <br>pdbalias atom ILE CD1 CD
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| - | <br>segment U
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| - | <br>{pdb ubqp.pdb}
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| - | <br>coordpdb ubqp.pdb U
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| - | <br>guesscoord
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| - | <br>writepdb ubq.pdb
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| - | <br>writepsf ubq.psf
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Latest revision as of 15:15, 21 July 2009
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