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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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| - | We open VMD, and lauch our protein
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| - | ==1. 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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| - |
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| - | ==2. 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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| - |
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| - | ==3. 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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| - | The "solvate package" will put the protein in a box of water. The -t option creates the water box dimensions such that
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| - | there is a layer of water 5 Angström in each direction from the atom with the largest coordinate in that direction. The -o option creates the output files our_prot_in_a_water_box .pdb and our_prot_in_a_water_box.psf.
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| - |
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| - |
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| - | ==4. Add ions ==
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| - | In VMD, we load the psf and the pdb created with the pgn. Under Extension/Modeling/Add Ions, and knowing the charge of the protein (for exemple -7), we add 7 atoms of Na.
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| - | Instead of concentrations, we click user defined to add 7 Na, and neutralize.
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| - |
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| - | [[Image: Ionization.jpg|thumb|Ionization]]
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| - |
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| - | ==5. Measurement of the water box coordinates==
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| - | In VMDload the our_prot_in_a_water_box.psf and the our_prot_in_a_water_box.pdb. This will display our protein in a water box.
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| - | In the VMD TkCon window type:
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| - | : set everyone [atomselect top all]
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| - | : measure minmax $everyone
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| - | This gives the minimum and maximum values of x, y and z coordinates of the entire protein-water system, relative to the origin of the coordinate system.
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| - | The center of the water box may be determined by typing:
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| - | : measure center $everyone
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| - | These coordinates have to be kept and recorded for the referential.
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| - | The necessary pdb and psf files must now be copied into a new folder, called common. We will store the files there so we have a single directory from which to access them, and so that we do not need to keep multiple copies of them.
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| - | ==6. Simulation with Periodic Boundary Conditions ==
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| - | The use of periodic boundary conditions are effective in eliminating surface interaction of the water molecules and creating a more faithful representation of the in vivo environment than a water sphere surrounded by vacuum provides.
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| - | We first create a configuration file:
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| - | Fromthe tutorial of VMND, we can download the configuration files for the minimization and equilibration of the protein
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| - | in a water box.
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| - | Look at the tutorial for a more detailed explanation of the different parameters listed.
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| - | The simulation can be run by typing in a Terminal window:
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| - | : namd2 our_prot_configuration_file.conf > output_file.log
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| - | Output of the water sphere minimization-equilibration simulation will yield eleven output files. See the tutorial for a more detailed explanation of each file.
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| - |
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| - | ==7. Make a movie==
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| - | Open VMD,
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| - | [[Media: Movie_generation.jpg]]
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| - | </div><div CLASS="epfl09bouchon"></div>
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