Removing Water Molecules

1

In a Terminal window, set your current directory as namd-tutorial-files using the cd command. Open a new session of VMD by clicking Start $\rightarrow$ Programs $\rightarrow$ VMD. Choose the Extensions $\rightarrow$ Tk Console menu item and navigate to the same directory there.

2

Choose the File $\rightarrow$ New Molecule... menu item of VMD. In the Molecule File Browser use the Browse... button to find the file ubq_ws.psf in the common directory. Load it by pressing the Load button. If you do not find the file, look for it in the common/example-output/ directory.

3

In the VMD Main window your molecule should appear (ID 0).

4

In the Molecule File Browser window, use the Browse... and the Load buttons load the file 1-2-sphere/ubq_ws_eq.restart.coor into your psf file. Be certain that the Load files for: field says 0:ubq_ws.psf. If you have not done that exercise, a copy of the corresponding output files is provided in the subdirectory 1-2-sphere/example-output/. When you are done, close the Molecule File Browser window.

Now you have the equilibrated ubiquitin in a water sphere loaded in VMD. The next step is to eliminate the water.

5

In the VMD TkCon window, type the following commands:

set selprotein [atomselect top protein]
$selprotein writepdb common/ubq_ww_eq.pdb

You have created a pdb file that contains the equilibrated protein without water.

6

Delete the current molecule by selecting it in the VMD Main window and choosing the Molecule $\rightarrow$ Delete Molecule menu item and keep VMD opened.