Simulation

We start with the PDB file of the protein, obtained through the Protein Data Bank.

We open VMD, and lauch our protein

1. 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.

2. 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

In a Terminal window, type the following command:

> vmd -dispdev text -e our_protein.pgn

This will run the package psfgen on the file ubq.pgn and generate the psf and the pdb file of ubiquitin with hydrogens. 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.

3. Solvating the Protein

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.

In the VMD Main window, open the Tk Console, and type:

package require solvate

solvate our_protein.psf our_protein.pdb -t 5 -o our_prot_in_a_water_box

The "solvate package" will put the protein in a box of water. The -t option creates the water box dimensions such that 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.

4. Add ions

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. Instead of concentrations, we click user defined to add 7 Na, and neutralize.

Ionization

5. Measurement of the water box coordinates

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. In the VMD TkCon window type:

set everyone [atomselect top all]

measure minmax $everyone

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.

The center of the water box may be determined by typing:

measure center $everyone

These coordinates have to be kept and recorded for the referential.

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.

6. Simulation with Periodic Boundary Conditions

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.

We first create a configuration file: Fromthe tutorial of VMND, we can download the configuration files for the minimization and equilibration of the protein in a water box. Look at the tutorial for a more detailed explanation of the different parameters listed.

The simulation can be run by typing in a Terminal window:

namd2 our_prot_configuration_file.conf > output_file.log

Output of the water sphere minimization-equilibration simulation will yield eleven output files. See the tutorial for a more detailed explanation of each file.

7. Make a movie

Open VMD, Media: Movie_generation.jpg‎