Solvating the Protein

Now, the protein needs to be solvated, i.e., put inside water, to more closely resemble the cellular environment. You will do so in two ways, placing ubiquitin in:

• a water sphere in vacuum, in preparation for minimization and equilibration without periodic boundary conditions.
• a water box, in preparation for minimization and equilibration with periodic boundary conditions.

Ubiquitin in a Water Sphere

You will utilize a prepared tcl script to create the water sphere. It is called wsphere.tcl and is located in your 1-1-build directory. The syntax of the script itself is given in Appendix G.

1

In a Unix Terminal window in your 1-1-build directory, type vmd -dispdev text -e wsphere.tcl. This will call the script, which will place ubiquitin in the smallest possible water sphere which completely immerses the protein.

2

The output of the wsphere.tcl file will be the center of mass and radius of the sphere. Record these numbers. The script will have created the pdb and psf files ubq_ws.pdb and ubq_ws.psf, respectively, of ubiquitin in a water sphere. They will be in your 1-1-build directory. Check this by typing ls.

Ubiquitin in a Water Box

1

Launch the graphical version of VMD by typing vmd in the Unix Terminal window.

2

In the VMD Main window, click Extensions $\rightarrow$ tkcon. In the VMD TkCon window of your VMD session type:

package require solvate
solvate ubq.psf ubq.pdb -t 5 -o ubq_wb

The package require solvate command simply places the solvate package in the correct place, so that VMD will be able to call it.
The solvate package will put your protein (described in ubq.psf and ubq.pdb) in a box of water. The -t option creates the water box dimensions such that there is a layer of water 5Å in each direction from the atom with the largest coordinate in that direction. The -o option creates the output files ubq_wb.pdb and ubq_wb.psf for ubiquitin with the water box. You will also obtain the files combine.pdb and combine.psf which may be eliminated. They are intermediate files used by the solvate program to transport information into VMD.

3

In the VMD Main window, click File $\rightarrow$ New Molecule. In the Molecule File Browser use the Browse... button to find the file ubq_wb.pdb. Load it by pressing the Load button.

4

In the same Molecule File Browser, browse for ubq_wb.psf and load it. This will load the structural information into VMD. In the display, check if the water box surrounds ubiquitin, and demonstrate to yourself that the hydrogen atoms now exist.

5

In the VMD TkCon window type:

set everyone [atomselect top all]
measure minmax $everyone

This analyzes all atoms in the system and gives you the minimum and maximum values of $x$, $y$ and $z$ coordinates of the entire protein-water system.

6

These values are defined relative to the origin of the coordinate system, set by the initial pdb file, 1UBQ.pdb. The center of the water box may be determined by calculating the midpoint of each of the three sides in the coordinate system. For example, if minimum and maximum values of $x$ are returned as 10.44 and 51.12, respectively, $x$-coordinate of the center of the box would be $\frac{51.12+10.44}{2} = 30.78$. Alternatively, one can use tcl scripting in VMD to find the center of the box by typing measure center $everyone in the VMD TkCon window. Determine the coordinates of the center of your water box and record these numbers.

7

Close VMD by typing exit in the vmd console window.

Figure 3: Ubiquitin in a water box and in a water sphere. Hydrogen atoms are colored black for contrast.

Now that you have the pdb and psf files for solvated ubiquitin, along with the parameter file for proteins in general, you only need a NAMD configuration file to be able to minimize and equilibrate your ubiquitin-water system. In the next two sections, you will edit a NAMD configuration file provided to you in order to gain a beginner's understanding of its function.

8

Before beginning the next section, you must copy the necessary pdb and psf files into your common folder. In a Unix Terminal window, type cp ubq.pdb ubq.psf ubq_w* ../common and hit Enter. Then, type ls ../common to see which files you have copied.