Removing Water Molecules

1

In a Unix Terminal window, set your current directory as namd-tutorial-files using the cd command. (In this directory you will find the structure already described in Fig. 1.) Open a new session of VMD by typing vmd.

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.

3

In the VMD Main window your molecule should appear (ID 0). Use the mouse to select it; the line will become highlighted in yellow.

4

Choose the File $\rightarrow$ Load Data Into Molecule... menu item and, using the Browse... and Load buttons, load the file
1-2-sphere/ubq_ws_eq.restart.coor. If you do not find the files, look for the provided output at the subdirectory 1-2-sphere/example-output/

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

5

Choose the Extensions $\rightarrow$ tkcon menu item, and 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 choosing the Molecule $\rightarrow$ Delete Molecule menu item and keep VMD opened.