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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
