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Team:EPF-Lausanne/Modeling/Movies
From 2009.igem.org
We start with the PDB file of the protein, obtained through the Protein Data Bank.
1. We open VMD, and lauch our protein
2. Creation of the pdb file In the Tk Console menu of VMD we open the VMD TkCon window, and type the following commands: set our_protein [atomselect top not water and not GOL] $our_protein writepdb our_protein.pdb
This will select all the protein except the water and except the glycerol, with the cofactor. We have created the file our_protein.pdb, which contains the coordinates of the protein alone without hydrogens. Quit VMD.
3. Creation of the psf file There is 2 ways to create a psf:
- in VCMD, Extensions → Modeling → Automatic PSF Builder
- We first make a pgn file, which will be the target of psfgen.
In a Terminal window, open a text editor and type: package require psfgen topology top all27 prot lipid.inp pdbalias residue HIS HSE pdbalias atom ILE CD1 CD segment U {pdb ubqp.pdb} coordpdb ubqp.pdb U guesscoord writepdb ubq.pdb writepsf ubq.psf
